[ { "id": "Q9BXL7-1.932.932", "start_pos": 932, "end_pos": 932, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RMNSNERVRIISGSPLGSLA", "down_seq": "SSLDATKLLTEKQEELDPES", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "2915281", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R932", "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:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9BXL7-1.916.916", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BXL7-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BXL7-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BXL7-1.926.926", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.967.967", "start_pos": 967, "end_pos": 967, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELDPESELGKNLSLIPYSLV", "down_seq": "AFYCERRRPVLFTPTVLAKT", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "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 (7).", "chr_id": "7", "chr_pos": "2913407", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R967", "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: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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9BXL7-1.968.968", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BXL7-1.973.973", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BXL7-1.975.975", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BXL7-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q9BXL7-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.968.968", "start_pos": 968, "end_pos": 968, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LDPESELGKNLSLIPYSLVR", "down_seq": "FYCERRRPVLFTPTVLAKTL", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "2913404", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A968", "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" } ] }, { "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": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BXL7-1.967.967", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q9BXL7-1.973.973", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BXL7-1.975.975", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BXL7-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BXL7-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.973.973", "start_pos": 973, "end_pos": 973, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELGKNLSLIPYSLVRAFYCE", "down_seq": "RRPVLFTPTVLAKTLVQRLL", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "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": "7", "chr_pos": "2913388", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R973", "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": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9BXL7-1.967.967", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BXL7-1.968.968", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BXL7-1.975.975", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q9BXL7-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BXL7-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.975.975", "start_pos": 975, "end_pos": 975, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GKNLSLIPYSLVRAFYCERR", "down_seq": "PVLFTPTVLAKTLVQRLLNS", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "2913382", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R975", "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: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": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9BXL7-1.967.967", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BXL7-1.968.968", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BXL7-1.973.973", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BXL7-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BXL7-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.977.977", "start_pos": 977, "end_pos": 977, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "NLSLIPYSLVRAFYCERRRP", "down_seq": "LFTPTVLAKTLVQRLLNSGG", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "2913377", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V977", "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" } ] }, { "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": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9BXL7-1.967.967", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BXL7-1.968.968", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q9BXL7-1.973.973", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BXL7-1.975.975", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BXL7-1.987.987", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.987.987", "start_pos": 987, "end_pos": 987, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BXL7", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RAFYCERRRPVLFTPTVLAK", "down_seq": "LVQRLLNSGGAMEFTICKSD", "snv": [ { "evidence": [ { "id": "Q9BXL7", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BXL7" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "7", "chr_pos": "2913346", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T987", "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: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: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": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BXL7-1.967.967", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q9BXL7-1.968.968", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q9BXL7-1.973.973", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9BXL7-1.975.975", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BXL7-1.977.977", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BXL7-1.1010.1010", "start_pos": 1010, "end_pos": 1010, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.iedb.org/epitope/Q9BXL7", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "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": "QRLLNSGGAMEFTICKSDIV", "down_seq": "RDEFLRRQKTETIIYSREKN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q9BXL7", "url": "https://www.iedb.org/epitope/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr1010" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BXL7-1.1009.1009", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BXL7-1.1020.1020", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BXL7-1.1027.1027", "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": "Q9BXL7-1.448.448", "start_pos": 448, "end_pos": 448, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IVNLESKLRRLSKDSNNLDQ", "down_seq": "LPRNLPVTIISQDFGDASPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser448" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9BXL7-1.429.429", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9BXL7-1.436.436", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9BXL7-1.440.440", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BXL7-1.446.446", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BXL7-1.454.454", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BXL7-1.457.457", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9BXL7-1.460.460", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BXL7-1.464.464", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BXL7-1.466.466", "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": "Q9BXL7-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DQSLPRNLPVTIISQDFGDA", "down_seq": "PRTNGQEADDSSTSEESPED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser466" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q9BXL7-1.446.446", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9BXL7-1.448.448", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9BXL7-1.454.454", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BXL7-1.457.457", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q9BXL7-1.460.460", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BXL7-1.464.464", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9BXL7-1.475.475", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BXL7-1.476.476", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BXL7-1.480.480", "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": "Q9BXL7-1.512.512", "start_pos": 512, "end_pos": 512, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "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": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" } ] }, { "title": "T-Cell Immunopeptidomes Reveal Cell Subtype Surface Markers Derived From Intracellular Proteins.", "journal": "Proteomics", "date": "2018-06", "authors": "Olsson Niclas, Schultz Liora M, Zhang Lichao, Khodadoust Michael S, Narayan Rupa, Czerwinski Debra K, Levy Ronald, Elias Joshua E", "evidence": [ { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "IEDB", "id": "193798", "url": "https://www.iedb.org/epitope/193798" }, { "database": "IEDB", "id": "572064", "url": "https://www.iedb.org/epitope/572064" }, { "database": "IEDB", "id": "727166", "url": "https://www.iedb.org/epitope/727166" }, { "database": "IEDB", "id": "930085", "url": "https://www.iedb.org/epitope/930085" } ], "reference": [ { "type": "PubMed", "id": "29493099", "url": "https://glygen.org/publication/PubMed/29493099" } ] }, { "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": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "IEDB", "id": "217450", "url": "https://www.iedb.org/epitope/217450" }, { "database": "IEDB", "id": "704208", "url": "https://www.iedb.org/epitope/704208" }, { "database": "IEDB", "id": "727166", "url": "https://www.iedb.org/epitope/727166" } ], "reference": [ { "type": "PubMed", "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "https://www.iedb.org/epitope/Q9BXL7", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29493099", "url": "https://glygen.org/publication/PubMed/29493099", "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": "PYHPPQRRMNLKGIQLQRAK", "down_seq": "PISLKRTSDFQAKGHEEEGT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "IEDB", "id": "Q9BXL7", "url": "https://www.iedb.org/epitope/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" }, { "database": "PubMed", "id": "29493099", "url": "https://glygen.org/publication/PubMed/29493099" }, { "database": "PubMed", "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261" } ], "site_lbl": "Ser512" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q9BXL7-1.500.500", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BXL7-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BXL7-1.528.528", "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": "Q9BXL7-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLKRTSDFQAKGHEEEGTDA", "down_seq": "PSSCGSLPITNSFTKMQPPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser535" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9BXL7-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BXL7-1.528.528", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BXL7-1.533.533", "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": "Q9BXL7-1.559.559", "start_pos": 559, "end_pos": 559, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of the CARMA1 linker controls NF-kappaB activation.", "journal": "Immunity", "date": "2005", "authors": "Sommer K, Guo B, Pomerantz JL, Bandaranayake AD, Moreno-Garcia ME, Ovechkina YL, Rawlings DJ", "evidence": [ { "database": "Reactome", "id": "R-HSA-1169091", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1169091" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q9BXL7", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BXL7", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CGSLPITNSFTKMQPPRSRS", "down_seq": "IMSITAEPPGNDSIVRRYKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P05771-1", "kinase_gene_name": "PRKCB", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "PubMed", "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855" } ], "site_lbl": "Ser559" }, { "kinase_uniprot_canonical_ac": "Q04759-1", "kinase_gene_name": "PRKCQ", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "PubMed", "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855" } ], "site_lbl": "Ser559" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by PKC/PRKCB and PKC/PRKCQ", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PRO", "id": "Q9BXL7", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser559" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q9BXL7-1.556.556", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BXL7-1.560.560", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BXL7-1.576.576", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BXL7-1.593.593", "start_pos": 593, "end_pos": 593, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "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": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IVRRYKEDAPHRSTVEEDND", "down_seq": "GGFDALDLDDDSHERYSFGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "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": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser593" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BXL7-1.576.576", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9BXL7-1.581.581", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BXL7-1.583.583", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q9BXL7-1.588.588", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BXL7-1.603.603", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BXL7-1.607.607", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BXL7-1.612.612", "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": "Q9BXL7-1.644.644", "start_pos": 644, "end_pos": 644, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of the CARMA1 linker controls NF-kappaB activation.", "journal": "Immunity", "date": "2005", "authors": "Sommer K, Guo B, Pomerantz JL, Bandaranayake AD, Moreno-Garcia ME, Ovechkina YL, Rawlings DJ", "evidence": [ { "database": "Reactome", "id": "R-HSA-1169091", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-1169091" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855" } ] }, { "title": "Dephosphorylation of Carma1 by PP2A negatively regulates T-cell activation.", "journal": "The EMBO journal", "date": "2011", "authors": "Eitelhuber AC, Warth S, Schimmack G, Duwel M, Hadian K, Demski K, Beisker W, Shinohara H, Kurosaki T, Heissmeyer V, Krappmann D", "evidence": [ { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "21157432", "url": "https://glygen.org/publication/PubMed/21157432" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21157432", "url": "https://glygen.org/publication/PubMed/21157432", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q9BXL7", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BXL7", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QSEGLDAYDLEQVNLMFRKF", "down_seq": "LERPFRPSVTSVGHVRGPGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P05771-1", "kinase_gene_name": "PRKCB", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "PubMed", "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855" } ], "site_lbl": "Ser644" }, { "kinase_uniprot_canonical_ac": "Q04759-1", "kinase_gene_name": "PRKCQ", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" }, { "database": "PubMed", "id": "16356855", "url": "https://glygen.org/publication/PubMed/16356855" }, { "database": "PubMed", "id": "21157432", "url": "https://glygen.org/publication/PubMed/21157432" } ], "site_lbl": "Ser644" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by PKC/PRKCB and PKC/PRKCQ", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PRO", "id": "Q9BXL7", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser644" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BXL7-1.626.626", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q9BXL7-1.642.642", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q9BXL7-1.650.650", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9BXL7-1.652.652", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9BXL7-1.660.660", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BXL7-1.886.886", "start_pos": 886, "end_pos": 886, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RALRNTLQPEEALSTSDPRV", "down_seq": "PRLSRASFLFGQLLQFVSRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser886" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q9BXL7-1.871.871", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q9BXL7-1.888.888", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BXL7-1.897.897", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BXL7-1.903.903", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BXL7-1.904.904", "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": "Q9BXL7-1.925.925", "start_pos": 925, "end_pos": 925, "uniprot_canonical_ac": "Q9BXL7-1", "length": 1154, "uniprot_id": "CAR11_HUMAN", "protein_name": "Caspase recruitment domain-containing protein 11", "refseq_ac": "NP_001311210", "refseq_name": "caspase recruitment domain-containing protein 11", "gene_name": "CARD11", "gene_names_uniprotkb": "CARD11; CARMA1", "gene_names_refseq": "BENTA; BIMP3; CARD11; CARMA1; IMD11A; IMD11; PPBL", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "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": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] } ], "crossref": [ { "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7", "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": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSENKYKRMNSNERVRIISG", "down_seq": "PLGSLARSSLDATKLLTEKQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9BXL7", "url": "https://www.uniprot.org/uniprotkb/Q9BXL7" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "Q9BXL7", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BXL7" } ], "site_lbl": "Ser925" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "285", "end_pos": "285" }, { "start_pos": "871", "end_pos": "871" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "28", "end_pos": "28" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1009", "end_pos": "1009" }, { "start_pos": "1020", "end_pos": "1020" }, { "start_pos": "1027", "end_pos": "1027" }, { "start_pos": "1033", "end_pos": "1033" }, { "start_pos": "1035", "end_pos": "1035" }, { "start_pos": "1046", "end_pos": "1046" }, { "start_pos": "1047", "end_pos": "1047" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1077", "end_pos": "1077" }, { "start_pos": "1101", "end_pos": "1101" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1133", "end_pos": "1133" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1144", "end_pos": "1144" }, { "start_pos": "149", "end_pos": "149" }, { "start_pos": "14", "end_pos": "14" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "187", "end_pos": "187" }, { "start_pos": "207", "end_pos": "207" }, { "start_pos": "209", "end_pos": "209" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "239", "end_pos": "239" }, { "start_pos": "251", "end_pos": "251" }, { "start_pos": "257", "end_pos": "257" }, { "start_pos": "261", "end_pos": "261" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "275", "end_pos": "275" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "291", "end_pos": "291" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "309", "end_pos": "309" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "356", "end_pos": "356" }, { "start_pos": "357", "end_pos": "357" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "382", "end_pos": "382" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "411", "end_pos": "411" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "425", "end_pos": "425" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "436", "end_pos": "436" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "446", "end_pos": "446" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "475", "end_pos": "475" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "500", "end_pos": "500" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "533", "end_pos": "533" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "583", "end_pos": "583" }, { "start_pos": "588", "end_pos": "588" }, { "start_pos": "603", "end_pos": "603" }, { "start_pos": "607", "end_pos": "607" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "623", "end_pos": "623" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "642", "end_pos": "642" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "675", "end_pos": "675" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "688", "end_pos": "688" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "694", "end_pos": "694" }, { "start_pos": "702", "end_pos": "702" }, { "start_pos": "720", "end_pos": "720" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "756", "end_pos": "756" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "789", "end_pos": "789" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "818", "end_pos": "818" }, { "start_pos": "834", "end_pos": "834" }, { "start_pos": "838", "end_pos": "838" }, { "start_pos": "862", "end_pos": "862" }, { "start_pos": "871", "end_pos": "871" }, { "start_pos": "888", "end_pos": "888" }, { "start_pos": "897", "end_pos": "897" }, { "start_pos": "903", "end_pos": "903" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "907", "end_pos": "907" }, { "start_pos": "916", "end_pos": "916" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "926", "end_pos": "926" }, { "start_pos": "932", "end_pos": "932" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "968", "end_pos": "968" }, { "start_pos": "973", "end_pos": "973" }, { "start_pos": "975", "end_pos": "975" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "987", "end_pos": "987" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1010", "end_pos": "1010" }, { "start_pos": "448", "end_pos": "448" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "512", "end_pos": "512" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "559", "end_pos": "559" }, { "start_pos": "593", "end_pos": "593" }, { "start_pos": "644", "end_pos": "644" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "886", "end_pos": "886" }, { "start_pos": "925", "end_pos": "925" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9BXL7-1.907.907", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q9BXL7-1.916.916", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BXL7-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q9BXL7-1.926.926", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BXL7-1.932.932", "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": "P55061-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "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": "P55061", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P55061" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "P55061", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P55061" }, { "database": "O-GlcNAc Atlas", "id": "P55061", "url": "https://oglcnac.org/atlas/detail/P55061" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P55061", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P55061", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P55061", "url": "https://oglcnac.org/atlas/detail/P55061", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1425356544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1425356544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1425356544", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1425356544", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NIFDRKINFDALLKFSHITP", "down_seq": "TQQHLKKVYASFALCMFVAA", "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": "Ser22", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "P55061", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P55061" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "id": "P55061", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P55061" } ] } ], "snv": [ { "evidence": [ { "id": "rs1425356544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1425356544" }, { "id": "rs1425356544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1425356544" } ], "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": "49752980", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S22", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P55061-1.4.4", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P55061-1.209.209", "start_pos": 209, "end_pos": 209, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The C terminus of Bax inhibitor-1 forms a Ca2+-permeable channel pore.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Bultynck G, Kiviluoto S, Henke N, Ivanova H, Schneider L, Rybalchenko V, Luyten T, Nuyts K, De Borggraeve W, Bezprozvanny I, Parys JB, De Smedt H, Missiaen L, Methner A", "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "reference": [ { "type": "PubMed", "id": "22128171", "url": "https://glygen.org/publication/PubMed/22128171" } ] } ], "crossref": [ { "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22128171", "url": "https://glygen.org/publication/PubMed/22128171", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TQLIIEKAEHGDQDYIWHCI", "down_seq": "LFLDFITVFRKLMMILAMNE", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolishes calcium flux properties.", "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" }, { "database": "PubMed", "id": "22128171", "url": "https://glygen.org/publication/PubMed/22128171" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "P55061-1.213.213", "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": "P55061-1.213.213", "start_pos": 213, "end_pos": 213, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The C terminus of Bax inhibitor-1 forms a Ca2+-permeable channel pore.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Bultynck G, Kiviluoto S, Henke N, Ivanova H, Schneider L, Rybalchenko V, Luyten T, Nuyts K, De Borggraeve W, Bezprozvanny I, Parys JB, De Smedt H, Missiaen L, Methner A", "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "reference": [ { "type": "PubMed", "id": "22128171", "url": "https://glygen.org/publication/PubMed/22128171" } ] } ], "crossref": [ { "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22128171", "url": "https://glygen.org/publication/PubMed/22128171", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "IEKAEHGDQDYIWHCIDLFL", "down_seq": "FITVFRKLMMILAMNEKDKK", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolishes calcium flux properties.", "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" }, { "database": "PubMed", "id": "22128171", "url": "https://glygen.org/publication/PubMed/22128171" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P55061-1.209.209", "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": "P55061-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61941194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61941194", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61941194", "url": "https://www.ensembl.org/id/rs61941194", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P55061", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P55061", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs773034667", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773034667", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773034667", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773034667", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773034667", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773034667", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FAFLTGVGLGPALEFCIAVN", "down_seq": "SILPTAFMGTAMIFTCFTLS", "snv": [ { "evidence": [ { "id": "rs61941194", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61941194" }, { "id": "rs61941194", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs61941194" } ], "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": "12", "chr_pos": "49758272", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P111", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P55061", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P55061" }, { "id": "rs773034667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773034667" }, { "id": "rs773034667", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773034667" }, { "id": "rs773034667", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773034667" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "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": "12", "chr_pos": "49758271", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P111", "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": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P55061-1.129.129", "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": 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": "P55061-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1049598119", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1049598119", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1049598119", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1049598119#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1049598119", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1049598119", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VNPSILPTAFMGTAMIFTCF", "down_seq": "LSALYARRRSYLFLGGILMS", "snv": [ { "evidence": [ { "id": "rs1049598119", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1049598119" }, { "id": "rs1049598119", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1049598119#frequency_tab" }, { "id": "rs1049598119", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1049598119" } ], "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": "12", "chr_pos": "49758433", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T129", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P55061-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P55061-1.175.175", "start_pos": 175, "end_pos": 175, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757393612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757393612", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757393612", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757393612", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757393612", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757393612#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs757393612", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757393612", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LLSSLGNVFFGSIWLFQANL", "down_seq": "VGLVVMCGFVLFDTQLIIEK", "snv": [ { "evidence": [ { "id": "rs757393612", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757393612" }, { "id": "rs757393612", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757393612" }, { "id": "rs757393612", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs757393612#frequency_tab" }, { "id": "rs757393612", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757393612" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLY->NLC).", "chr_id": "12", "chr_pos": "49759231", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y175", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "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": "P55061-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P55061", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P55061", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MNI", "down_seq": "DRKINFDALLKFSHITPSTQ", "snv": [ { "evidence": [ { "id": "P55061", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P55061" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIF->NIS).", "chr_id": "12", "chr_pos": "49752504", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F4", "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": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "P55061-1.22.22", "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": "P55061-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P55061-1", "length": 237, "uniprot_id": "BI1_HUMAN", "protein_name": "Bax inhibitor 1", "refseq_ac": "NP_001092046", "refseq_name": "bax inhibitor 1 isoform 2", "gene_name": "TMBIM6", "gene_names_uniprotkb": "TMBIM6; BI1; TEGT", "gene_names_refseq": "BAXI1; BI-1; TEGT; TMBIM6", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P55061", "url": "https://www.uniprot.org/uniprotkb/P55061" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs186525370", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs186525370", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs186525370", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs186525370", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs186525370", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs186525370", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs186525370", "url": "https://www.ncbi.nlm.nih.gov/snp/rs186525370#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs186525370", "url": "http://gnomad.broadinstitute.org/awesome?query=rs186525370", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LLSALGSLILMIWLMATPHS", "down_seq": "ETEQKRLGLLAGFAFLTGVG", "snv": [ { "evidence": [ { "id": "rs186525370", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs186525370" }, { "id": "rs186525370", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs186525370" }, { "id": "rs186525370", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs186525370" }, { "id": "rs186525370", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs186525370#frequency_tab" }, { "id": "rs186525370", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs186525370" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HET->NET).", "chr_id": "12", "chr_pos": "49755701", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "H78", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "22", "end_pos": "22" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "209", "end_pos": "209" }, { "start_pos": "213", "end_pos": "213" } ] }, { "type": "snv", "site_list": [ { "start_pos": "111", "end_pos": "111" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "175", "end_pos": "175" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "78", "end_pos": "78" } ] } ], "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": "Q9BSU1-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9BSU1-1", "length": 422, "uniprot_id": "PHAF1_HUMAN", "protein_name": "Phagosome assembly factor 1", "refseq_ac": "NP_001307469", "refseq_name": "phagosome assembly factor 1 isoform a", "gene_name": "PHAF1", "gene_names_uniprotkb": "PHAF1; C16orf6; C16orf70", "gene_names_refseq": "C16orf6; C16orf70; LIN10; MYTHO; PHAF1; lin-10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BSU1", "url": "https://www.uniprot.org/uniprotkb/Q9BSU1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy.", "journal": "Nature communications", "date": "2025-02-02", "authors": "Zhang Na, Meng Yang, Mao Song, Ni Huiling, Huang Canhua, Shen Licong, Fu Kun, Lv Lu, Yu Chunhong, Meekrathok Piyanat, Kuang Chunmei, Chen Fang, Zhang Yu, Yuan Kai", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9BSU1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BSU1" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BSU1", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BSU1", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q9BSU1", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BSU1" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "409", "end_pos": "409" } ] } ], "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": "Q9BSU1-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "Q9BSU1-1", "length": 422, "uniprot_id": "PHAF1_HUMAN", "protein_name": "Phagosome assembly factor 1", "refseq_ac": "NP_001307469", "refseq_name": "phagosome assembly factor 1 isoform a", "gene_name": "PHAF1", "gene_names_uniprotkb": "PHAF1; C16orf6; C16orf70", "gene_names_refseq": "C16orf6; C16orf70; LIN10; MYTHO; PHAF1; lin-10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BSU1", "url": "https://www.uniprot.org/uniprotkb/Q9BSU1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BSU1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BSU1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PMMPLSCFLGNVYAESVDVL", "down_seq": "DGTGPAGLRLRLLAAGCGPG", "snv": [ { "evidence": [ { "id": "Q9BSU1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BSU1" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "67134419", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R205", "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": "snv", "site_list": [ { "start_pos": "205", "end_pos": "205" }, { "start_pos": "409", "end_pos": "409" } ] } ], "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": "Q9BSU1-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q9BSU1-1", "length": 422, "uniprot_id": "PHAF1_HUMAN", "protein_name": "Phagosome assembly factor 1", "refseq_ac": "NP_001307469", "refseq_name": "phagosome assembly factor 1 isoform a", "gene_name": "PHAF1", "gene_names_uniprotkb": "PHAF1; C16orf6; C16orf70", "gene_names_refseq": "C16orf6; C16orf70; LIN10; MYTHO; PHAF1; lin-10", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BSU1", "url": "https://www.uniprot.org/uniprotkb/Q9BSU1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BSU1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BSU1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QRMIFEVMQNNHIASVTLYG", "down_seq": "PRPGSHLRTAELP", "snv": [ { "evidence": [ { "id": "Q9BSU1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BSU1" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "67147088", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P409", "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": "205", "end_pos": "205" }, { "start_pos": "409", "end_pos": "409" } ] } ], "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": "Q06330-1.455.455", "start_pos": 455, "end_pos": 455, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" }, { "database": "O-GlcNAc Atlas", "id": "Q06330", "url": "https://oglcnac.org/atlas/detail/Q06330" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" }, { "database": "O-GlcNAc Atlas", "id": "Q06330", "url": "https://oglcnac.org/atlas/detail/Q06330" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" } ], "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": "Q06330", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330", "database": "O-GlcNAc Database", "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": "30059200", "url": "https://glygen.org/publication/PubMed/30059200", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "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" ] }, { "id": "Q06330", "url": "https://oglcnac.org/atlas/detail/Q06330", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYSTSLTFTYTPEPGPRPHC", "down_seq": "AAGAILRANSSQVPPNESNT", "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": "Ser455", "evidence": [ { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "Q06330", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q06330" }, { "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": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "Q06330", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q06330" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q06330-1.500.500", "start_pos": 500, "end_pos": 500, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q06330", "url": "https://oglcnac.org/atlas/detail/Q06330" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] } ], "crossref": [ { "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q06330", "url": "https://oglcnac.org/atlas/detail/Q06330", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SYTNASTNSTSVTSSTATVV", "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": "Ser500", "evidence": [ { "id": "32938750", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32938750" }, { "id": "Q06330", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q06330" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q06330-1.490.490", "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": "Q06330-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06330", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ADLCIASGTKVALFNRLRSQ", "down_seq": "VSTRYLHVEGGNFHASSQQW", "snv": [ { "evidence": [ { "id": "Q06330", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "26424396", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "T197", "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: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": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "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": "Q06330-1.228.228", "start_pos": 228, "end_pos": 228, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761342901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761342901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761342901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761342901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761342901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761342901", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GNFHASSQQWGAFFIHLLDD", "down_seq": "ESEGEEFTVRDGYIHYGQTV", "snv": [ { "evidence": [ { "id": "rs761342901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761342901" }, { "id": "rs761342901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761342901" }, { "id": "rs761342901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761342901" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DES->NES).", "chr_id": "4", "chr_pos": "26424639", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D228", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q06330-1.230.230", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q06330-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06330", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "IIQFQATPCPKEPNKEMIND", "down_seq": "ASWTIISTDKAEYTFYEGMG", "snv": [ { "evidence": [ { "id": "Q06330", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "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": "4", "chr_pos": "26429943", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G325", "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": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q06330-1.339.339", "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": "Q06330-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763438082", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763438082", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763438082", "url": "https://www.ensembl.org/id/rs763438082", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GPVLAPVTPVPVVESLQLNG", "down_seq": "GDVAMLELTGQNFTPNLRVW", "snv": [ { "evidence": [ { "id": "rs763438082", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763438082" }, { "id": "rs763438082", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs763438082" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGG->NGS).", "chr_id": "4", "chr_pos": "26430428", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G365", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "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": "Q06330-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06330", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PSPGKFGERPPPKRLTREAM", "down_seq": "NYLKERGDQTVLILHAKVAQ", "snv": [ { "evidence": [ { "id": "Q06330", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330" } ], "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 (3).", "chr_id": "4", "chr_pos": "26406186", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R37", "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": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "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": "Q06330-1.476.476", "start_pos": 476, "end_pos": 476, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760469930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760469930", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760469930", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760469930", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760469930", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760469930#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760469930", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760469930", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AAGAILRANSSQVPPNESNT", "down_seq": "SEGSYTNASTNSTSVTSSTA", "snv": [ { "evidence": [ { "id": "rs760469930", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760469930" }, { "id": "rs760469930", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760469930" }, { "id": "rs760469930", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760469930#frequency_tab" }, { "id": "rs760469930", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760469930" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "4", "chr_pos": "26430931", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N476", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q06330-1.490.490", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q06330-1.490.490", "start_pos": 490, "end_pos": 490, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1675930053", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1675930053", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1675930053", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1675930053#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PNESNTNSEGSYTNASTNST", "down_seq": "VTSSTATVVS", "snv": [ { "evidence": [ { "id": "rs1675930053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1675930053" }, { "id": "rs1675930053", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1675930053#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 (SVT->NVT).", "chr_id": "4", "chr_pos": "26430973", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S490", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q06330-1.476.476", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q06330-1.500.500", "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": "Q06330-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q06330", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs147349346", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147349346", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs147349346", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147349346", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs147349346", "url": "https://www.ncbi.nlm.nih.gov/snp/rs147349346#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs147349346", "url": "http://gnomad.broadinstitute.org/awesome?query=rs147349346", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs147349346", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs147349346", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PPCVYLMGSGWKKKKEQMER", "down_seq": "GCSEQESQPCAFIGIGNSDQ", "snv": [ { "evidence": [ { "id": "Q06330", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q06330" }, { "id": "rs147349346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147349346" }, { "id": "rs147349346", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs147349346" }, { "id": "rs147349346", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs147349346#frequency_tab" }, { "id": "rs147349346", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs147349346" }, { "id": "rs147349346", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs147349346" } ], "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 (DGC->NGC).", "chr_id": "4", "chr_pos": "26415548", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D90", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "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": "Q06330-1.230.230", "start_pos": 230, "end_pos": 230, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "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": "Q06330-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "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": "Q06330-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] } ], "crossref": [ { "id": "Q06330", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278", "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": "FHASSQQWGAFFIHLLDDDE", "down_seq": "EGEEFTVRDGYIHYGQTVKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06330", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ], "site_lbl": "Ser230" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q06330-1.228.228", "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": "Q06330-1.339.339", "start_pos": 339, "end_pos": 339, "uniprot_canonical_ac": "Q06330-1", "length": 500, "uniprot_id": "SUH_HUMAN", "protein_name": "Recombining binding protein suppressor of hairless", "refseq_ac": "NP_005340", "refseq_name": "recombining binding protein suppressor of hairless isoform 1", "gene_name": "RBPJ", "gene_names_uniprotkb": "RBPJ; IGKJRB1; IGKJRB; RBPJK; RBPSUH", "gene_names_refseq": "AOS3; CBF-1; CBF1; IGKJRB1; IGKJRB; KBF2; RBP-J kappa; RBP-JK; RBP-J; RBPJK; RBPJ; RBPSUH; SUH; csl", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q06330", "url": "https://www.uniprot.org/uniprotkb/Q06330" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Presenilin-2 regulates the degradation of RBP-Jk protein through p38 mitogen-activated protein kinase.", "journal": "Journal of cell science", "date": "2012-03-01", "authors": "Kim Su-Man, Kim Mi-Yeon, Ann Eun-Jung, Mo Jung-Soon, Yoon Ji-Hye, Park Hee-Sae", "evidence": [ { "database": "iPTMnet", "id": "Q06330", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330" } ], "reference": [ { "type": "PubMed", "id": "22302987", "url": "https://glygen.org/publication/PubMed/22302987" } ] } ], "crossref": [ { "id": "Q06330", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "22302987", "url": "https://glygen.org/publication/PubMed/22302987", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KEMINDGASWTIISTDKAEY", "down_seq": "FYEGMGPVLAPVTPVPVVES", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q06330", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q06330" }, { "database": "PubMed", "id": "22302987", "url": "https://glygen.org/publication/PubMed/22302987" } ], "site_lbl": "Thr339" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "455", "end_pos": "455" }, { "start_pos": "500", "end_pos": "500" } ] }, { "type": "snv", "site_list": [ { "start_pos": "197", "end_pos": "197" }, { "start_pos": "228", "end_pos": "228" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "90", "end_pos": "90" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "230", "end_pos": "230" }, { "start_pos": "339", "end_pos": "339" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q06330-1.325.325", "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": "P60228-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "title": "Comparative analysis of Cu (I)-catalyzed alkyne-azide cycloaddition (CuAAC) and strain-promoted alkyne-azide cycloaddition (SPAAC) in O-GlcNAc proteomics.", "journal": "Electrophoresis", "date": "2016", "authors": "Li S, Zhu H, Wang J, Wang X, Li X, Ma C, Wen L, Yu B, Wang Y, Li J, Wang PG", "evidence": [ { "database": "O-GlcNAc Database", "id": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "reference": [ { "type": "PubMed", "id": "26853435", "url": "https://glygen.org/publication/PubMed/26853435" } ] }, { "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "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": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Mannose Inhibits NSCLC Growth and Inflammatory Microenvironment by Regulating Gut Microbiota and Targeting OGT/hnRNP R/JUN/IL-8 Axis.", "journal": "International journal of biological sciences", "date": "2025", "authors": "Jin Haoyi, He Huanghe, Li Jijia, Liu Xi, Cai Qi, Shi Jiang, Hao Zhexue, He Jianxing", "evidence": [ { "database": "O-GlcNAc Database", "id": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" } ], "reference": [ { "type": "PubMed", "id": "39990658", "url": "https://glygen.org/publication/PubMed/39990658" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P60228", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228", "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": "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": "26853435", "url": "https://glygen.org/publication/PubMed/26853435", "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": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39990658", "url": "https://glygen.org/publication/PubMed/39990658", "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": "P60228", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P60228" }, { "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": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "26853435", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26853435" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "39990658", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39990658" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "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": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P60228-1.312.312", "start_pos": 312, "end_pos": 312, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Isolation of the Schizosaccharomyces pombe proteasome subunit Rpn7 and a structure-function study of the proteasome-COP9-initiation factor domain.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Sha Z, Yen HC, Scheel H, Suo J, Hofmann K, Chang EC", "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "reference": [ { "type": "PubMed", "id": "17761670", "url": "https://glygen.org/publication/PubMed/17761670" } ] } ], "crossref": [ { "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17761670", "url": "https://glygen.org/publication/PubMed/17761670", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ITEFVECLYVNFDFDGAQKK", "down_seq": "RECESVLVNDFFLVACLEDF", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Promotes nuclear accumulation.", "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "PubMed", "id": "17761670", "url": "https://glygen.org/publication/PubMed/17761670" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "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": "P60228-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P60228", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QQRTWLIHWSLFVFFNHPKG", "down_seq": "DNIIDLFLYQPQYLNAIQTM", "snv": [ { "evidence": [ { "id": "P60228", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228" } ], "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": "8", "chr_pos": "108228304", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R229", "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: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": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "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": "P60228-1.268.268", "start_pos": 268, "end_pos": 268, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P60228", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TMCPHILRYLTTAVITNKDV", "down_seq": "KRRQVLKDLVKVIQQESYTY", "snv": [ { "evidence": [ { "id": "P60228", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "8", "chr_pos": "108217381", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R268", "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" } ] }, { "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": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P60228-1.271.271", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P60228-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P60228", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PHILRYLTTAVITNKDVRKR", "down_seq": "QVLKDLVKVIQQESYTYKDP", "snv": [ { "evidence": [ { "id": "P60228", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "108217372", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R271", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P60228-1.268.268", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P60228-1.428.428", "start_pos": 428, "end_pos": 428, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P60228", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "TKSLSFRSQMLAMNIEKKLN", "down_seq": "NSRSEAPNWATQDSGFY", "snv": [ { "evidence": [ { "id": "P60228", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P60228" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "108203000", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q428", "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: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": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "P60228-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P60228-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P60228-1.445.445", "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": "P60228-1.161.161", "start_pos": 161, "end_pos": 161, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "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": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228", "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": "CGNYSGAAEYLYFFRVLVPA", "down_seq": "DRNALSSLWGKLASEILMQN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr161" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "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": "P60228-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "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": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "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": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "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": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "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": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228", "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228", "database": "iPTMnet", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RLDAKIDSKLGHVVMGNNAV", "down_seq": "PYQQVIEKTKSLSFRSQMLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser399" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P60228-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AMNIEKKLNQNSRSEAPNWA", "down_seq": "QDSGFY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "site_lbl": "Thr439" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P60228-1.428.428", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P60228-1.442.442", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P60228-1.445.445", "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": "P60228-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "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": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IEKKLNQNSRSEAPNWATQD", "down_seq": "GFY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P60228", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P60228" } ], "site_lbl": "Ser442" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P60228-1.428.428", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P60228-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P60228-1.445.445", "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": "P60228-1.445.445", "start_pos": 445, "end_pos": 445, "uniprot_canonical_ac": "P60228-1", "length": 445, "uniprot_id": "EIF3E_HUMAN", "protein_name": "Eukaryotic translation initiation factor 3 subunit E", "refseq_ac": "NP_001559", "refseq_name": "eukaryotic translation initiation factor 3 subunit E", "gene_name": "EIF3E", "gene_names_uniprotkb": "EIF3E; EIF3S6; INT6", "gene_names_refseq": "EIF3-P48; EIF3E; EIF3S6; INT6; eIF3-p46", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KLNQNSRSEAPNWATQDSGF", "down_seq": "", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P60228", "url": "https://www.uniprot.org/uniprotkb/P60228" } ], "site_lbl": "Tyr445" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "312", "end_pos": "312" } ] }, { "type": "snv", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "268", "end_pos": "268" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "428", "end_pos": "428" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "161", "end_pos": "161" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "445", "end_pos": "445" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P60228-1.428.428", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P60228-1.439.439", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P60228-1.442.442", "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": "P08962-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DKVMSEFNNNFRQQMENYPK", "down_seq": "NHTASILDRMQADFKCCGAA", "glycosylation": [ { "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": "Asn129", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P08962-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P08962-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P08962-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P08962-1.130.130", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P08962-1.134.134", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P08962-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "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": "Tumor cells express pauci- and oligomannosidic N-glycans in glycoproteins recognized by the mannose receptor (CD206).", "journal": "Cellular and molecular life sciences : CMLS", "date": "2021", "authors": "Stavenhagen K, Laan LC, Gao C, Mehta AY, Heimburg-Molinaro J, Glickman JN, van Die I, Cummings RD", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "34089345", "url": "https://glygen.org/publication/PubMed/34089345" } ] }, { "title": "Tumor cells express pauci- and oligomannosidic N-glycans in glycoproteins recognized by the mannose receptor (CD206)", "journal": "Cell Mol Life Sci", "date": "2021", "authors": "Stavenhagen K., Laan L.C., Gao C., Mehta A.Y., Heimburg-Molinaro J., Glickman J.N., van Die I., Cummings R.D.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1007/s00018-021-03863-1", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" } ] }, { "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": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes.", "journal": "Journal of proteome research", "date": "2020", "authors": "Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Heck AJR", "evidence": [ { "database": "GlyConnect", "id": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ], "reference": [ { "type": "PubMed", "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "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": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962#ptm_processing" }, { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.", "journal": "Nature biotechnology", "date": "2003", "authors": "Zhang H, Li XJ, Martin DB, Aebersold R", "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962#ptm_processing" }, { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "reference": [ { "type": "PubMed", "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519" } ] }, { "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" } ] }, { "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": "34089345", "url": "https://glygen.org/publication/PubMed/34089345", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1007/s00018-021-03863-1", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1", "database": "DOI", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861", "database": "PubMed", "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": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs963741590", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs963741590", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs963741590", "url": "https://www.ncbi.nlm.nih.gov/snp/rs963741590#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs963741590", "url": "http://gnomad.broadinstitute.org/awesome?query=rs963741590", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KVMSEFNNNFRQQMENYPKN", "down_seq": "HTASILDRMQADFKCCGAAN", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G01650EU", "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": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "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": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G05962QB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G08290VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G10773YW", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G10819WX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G11314AS", "type": "N-linked;o-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G18647XP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G23294PN", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G23984SE", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G27058EU", "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": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "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": "G27915IV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "N", "relation": "attached", "comment": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "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": "G32788FZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G37399XV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "N", "relation": "attached", "comment": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G47644PP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G51640FO", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G57776ZU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G59924QI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G63041LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G68490OW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G74724QE", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G76295SF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G80479JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G81263BG", "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": "Asn130", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G83229XP", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G85269DF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G92062TF", "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": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G92275SC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NNHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G93718GY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G94854LT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G95177YH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G95865ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NnHTASILDR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "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": "G96091TT", "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": "high-energy collision-induced dissociation", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn130", "evidence": [ { "id": "34089345", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34089345" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1007/s00018-021-03863-1", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1007/s00018-021-03863-1" }, { "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": "Asn130", "evidence": [ { "id": "P08962", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P08962#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "12754519", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/12754519" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" } ] } ], "snv": [ { "evidence": [ { "id": "rs963741590", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs963741590" }, { "id": "rs963741590", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs963741590#frequency_tab" }, { "id": "rs963741590", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs963741590" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NHT->HHT).", "chr_id": "12", "chr_pos": "55726738", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N130", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P08962-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P08962-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P08962-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P08962-1.129.129", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P08962-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P08962-1.150.150", "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": 59 }, { "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": 56 }, { "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": 56 }, { "field": "fuzzy_n_linked;o_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked;o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked;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": 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": 58 }, { "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": 56 }, { "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": 56 }, { "field": "fuzzy_n_linked;o_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked;o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked;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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P08962-1.150.150", "start_pos": 150, "end_pos": 150, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ], "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" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088", "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": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962", "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": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1167328183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1167328183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1167328183", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1167328183#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "P08962", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1367384879", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367384879", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1367384879", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367384879", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NHTASILDRMQADFKCCGAA", "down_seq": "YTDWEKIPSMSKNRVPDSCC", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G01160VV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G01485JJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G02528FI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G03644CB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G05962QB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G06247RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G08290VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G09831WQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G10819WX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G11314AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G11870QZ", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G11911BT", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G12745LE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G13131HA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G16125XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G20528HD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G23294PN", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G23984SE", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G24528MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G25451PN", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G27915IV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G28622IK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G29545VG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G30970QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G31309XD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G32788FZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G34989PA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G35541EV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G37399XV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G37509XX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G37818NZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G40574BA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G40926MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAANYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G45526EA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G47644PP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G49906RN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G51653BI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G57776ZU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G59924QI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G60033FS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G63041LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G65414LI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G67164EE", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G69521XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G70888PK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G71463BG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G74724QE", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G76295SF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G79286RS", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80075MS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G80479JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G81637OR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G82443XX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G93718GY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G94390IS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G95865ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G96577RX", "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": "Asn150", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G99668VU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "G99679NM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "CCGAAnYTDWEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn150", "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": "Asn150", "evidence": [ { "id": "P08962", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P08962#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": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs1167328183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1167328183" }, { "id": "rs1167328183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1167328183#frequency_tab" } ], "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": "12", "chr_pos": "55726240", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N150", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P08962", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NYT->HYT).", "chr_id": "12", "chr_pos": "55726240", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N150", "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": "rs1367384879", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367384879" }, { "id": "rs1367384879", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367384879" } ], "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": "12", "chr_pos": "55726239", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N150", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1367384879", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367384879" }, { "id": "rs1367384879", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1367384879" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NYT->TYT).", "chr_id": "12", "chr_pos": "55726239", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N150", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P08962-1.130.130", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P08962-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P08962-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P08962-1.167.167", "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": 92 }, { "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": 91 }, { "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": 91 } ], "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": 91 }, { "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": 91 }, { "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": 91 } ], "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", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P08962-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ], "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" } ] }, { "title": "N-linked glycosylation enrichment for in-depth cell surface proteomics of diffuse large B-cell lymphoma subtypes.", "journal": "Molecular & cellular proteomics : MCP", "date": "2014", "authors": "Deeb SJ, Cox J, Schmidt-Supprian M, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1088", "url": "https://glyconnect.expasy.org/browser/proteins/1088", "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": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962", "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": "rs1877310884", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1877310884", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1877310884", "url": "https://www.ensembl.org/id/rs1877310884", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TDWEKIPSMSKNRVPDSCCI", "down_seq": "VTVGCGINFNEKAIHKEGCV", "glycosylation": [ { "glytoucan_ac": "G03644CB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G05962QB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G11314AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G16125XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G20210JR", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G23294PN", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G23984SE", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G27126ED", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G35541EV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G47644PP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G57776ZU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G62894KT", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G65414LI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G75568BH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G80479JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G85269DF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G92062TF", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1088", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1088" } ] }, { "glytoucan_ac": "G92275SC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G95865ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NRVPDSCCInVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G97993TU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "VPDSCCINVTVGCGINFNEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "evidence": [ { "id": "P08962", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P08962#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": "rs1877310884", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1877310884" }, { "id": "rs1877310884", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1877310884" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->TVT).", "chr_id": "12", "chr_pos": "55726173", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P08962-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P08962-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P08962-1.174.174", "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": 26 }, { "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": 25 }, { "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": 25 } ], "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": 25 }, { "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": 25 }, { "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": 25 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P08962-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "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": "WEKIPSMSKNRVPDSCCINV", "down_seq": "VGCGINFNEKAIHKEGCVEK", "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": "Thr174", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P08962-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P08962-1.172.172", "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": "P08962-1.79.79", "start_pos": 79, "end_pos": 79, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AVGVFLFLVAFVGCCGACKE", "down_seq": "YCLMITFAIFLSLIMLVEVA", "glycosylation": [ { "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": "Asn79", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P08962-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "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": "P08962", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08962" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P08962", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08962" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "P08962", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08962" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P08962", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08962", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "P08962", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P08962" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "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": "P08962-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1877429172", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1877429172", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1877429172", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1877429172#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VAAAIAGYVFRDKVMSEFNN", "down_seq": "FRQQMENYPKNNHTASILDR", "snv": [ { "evidence": [ { "id": "rs1877429172", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1877429172" }, { "id": "rs1877429172", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1877429172#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNN->NNS).", "chr_id": "12", "chr_pos": "55726773", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N118", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P08962-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P08962-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P08962-1.129.129", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P08962-1.130.130", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P08962-1.134.134", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P08962-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08962", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AAIAGYVFRDKVMSEFNNNF", "down_seq": "QQMENYPKNNHTASILDRMQ", "snv": [ { "evidence": [ { "id": "P08962", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962" } ], "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": "12", "chr_pos": "55726768", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R120", "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: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": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P08962-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P08962-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P08962-1.129.129", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P08962-1.130.130", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P08962-1.134.134", "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": "P08962-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1592530393", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1592530393", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1592530393", "url": "https://www.ensembl.org/id/rs1592530393", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FRDKVMSEFNNNFRQQMENY", "down_seq": "KNNHTASILDRMQADFKCCG", "snv": [ { "evidence": [ { "id": "rs1592530393", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1592530393" }, { "id": "rs1592530393", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1592530393" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYP->NYT).", "chr_id": "12", "chr_pos": "55726747", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P127", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P08962-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P08962-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P08962-1.129.129", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P08962-1.130.130", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P08962-1.134.134", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P08962-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08962", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EFNNNFRQQMENYPKNNHTA", "down_seq": "ILDRMQADFKCCGAANYTDW", "snv": [ { "evidence": [ { "id": "P08962", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962" } ], "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": "12", "chr_pos": "55726725", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S134", "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: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: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": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P08962-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P08962-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P08962-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P08962-1.129.129", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P08962-1.130.130", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P08962-1.150.150", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P08962-1.152.152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P08962-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1050717888", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1050717888", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1050717888", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1050717888#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TASILDRMQADFKCCGAANY", "down_seq": "DWEKIPSMSKNRVPDSCCIN", "snv": [ { "evidence": [ { "id": "rs1050717888", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1050717888" }, { "id": "rs1050717888", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1050717888#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 (NYT->NYI).", "chr_id": "12", "chr_pos": "55726233", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T152", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P08962-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P08962-1.150.150", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P08962-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P08962-1.172.172", "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": "P08962-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773718478", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773718478", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773718478", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773718478", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773718478", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773718478#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773718478", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773718478", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs773718478", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773718478", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GAANYTDWEKIPSMSKNRVP", "down_seq": "SCCINVTVGCGINFNEKAIH", "snv": [ { "evidence": [ { "id": "rs773718478", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773718478" }, { "id": "rs773718478", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773718478" }, { "id": "rs773718478", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773718478#frequency_tab" }, { "id": "rs773718478", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773718478" }, { "id": "rs773718478", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs773718478" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DSC->NSC).", "chr_id": "12", "chr_pos": "55726189", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D167", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P08962-1.150.150", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P08962-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P08962-1.172.172", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P08962-1.174.174", "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": "P08962-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "P08962-1", "length": 238, "uniprot_id": "CD63_HUMAN", "protein_name": "CD63 antigen", "refseq_ac": "NP_001244318", "refseq_name": "CD63 antigen isoform A", "gene_name": "CD63", "gene_names_uniprotkb": "CD63; MLA1; TSPAN30", "gene_names_refseq": "AD1; CD63; HOP-26; ME491; MLA1; OMA81H; Pltgp40; TSPAN30", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P08962", "url": "https://www.uniprot.org/uniprotkb/P08962" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P08962", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GIAFVEVLGIVFACCLVKSI", "down_seq": "SGYEVM", "snv": [ { "evidence": [ { "id": "P08962", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P08962" } ], "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": "12", "chr_pos": "55725582", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "R232", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "79", "end_pos": "79" } ] }, { "type": "snv", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "150", "end_pos": "150" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "232", "end_pos": "232" } ] } ], "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": "Q14683-1.1127.1127", "start_pos": 1127, "end_pos": 1127, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YLDGINYNCVAPGKRFRPMD", "down_seq": "LSGGEKTVAALALLFAIHSY", "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": "PMDNLSGGEK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1127", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14683-1.1114.1114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14683-1.1129.1129", "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": 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": "Q14683-1.549.549", "start_pos": 549, "end_pos": 549, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "crossref": [ { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2075689274", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2075689274", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2075689274", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2075689274#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2075689274", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2075689274", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KYQIAVTKVLGKNMDAIIVD", "down_seq": "EKTGRDCIQYIKEQRGEPET", "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": "Ser549", "evidence": [ { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "Q14683", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q14683" } ] } ], "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" }, { "id": "rs2075689274", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2075689274" }, { "id": "rs2075689274", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2075689274#frequency_tab" }, { "id": "rs2075689274", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2075689274" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "23", "chr_pos": "53405856", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S549", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14683-1.722.722", "start_pos": 722, "end_pos": 722, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" }, { "database": "O-GlcNAc Atlas", "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "title": "Comparative O-GlcNAc Proteomic Analysis Reveals a Role of O-GlcNAcylated SAM68 in Lung Cancer Aggressiveness.", "journal": "Cancers", "date": "2022", "authors": "Lin CH, Liao CC, Wang SY, Peng CY, Yeh YC, Chen MY, Chou TY", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "reference": [ { "type": "PubMed", "id": "35008409", "url": "https://glygen.org/publication/PubMed/35008409" } ] }, { "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" }, { "database": "O-GlcNAc Atlas", "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "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": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35008409", "url": "https://glygen.org/publication/PubMed/35008409", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "QSQAHGLQMRLKYSQSDLEQ", "down_seq": "KTRHLALNLQEKSKLESELA", "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": "Thr722", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q14683", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35008409", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35008409" }, { "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q14683", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q14683" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr722" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "glycosylation_flag", "phosphorylation_flag" ], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q14683-1.711.711", "categories": [ "snv_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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14683-1.882.882", "start_pos": 882, "end_pos": 882, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" }, { "database": "O-GlcNAc Atlas", "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "title": "Comparative O-GlcNAc Proteomic Analysis Reveals a Role of O-GlcNAcylated SAM68 in Lung Cancer Aggressiveness.", "journal": "Cancers", "date": "2022", "authors": "Lin CH, Liao CC, Wang SY, Peng CY, Yeh YC, Chen MY, Chou TY", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "reference": [ { "type": "PubMed", "id": "35008409", "url": "https://glygen.org/publication/PubMed/35008409" } ] }, { "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" } ], "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": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" }, { "database": "O-GlcNAc Atlas", "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "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": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35008409", "url": "https://glygen.org/publication/PubMed/35008409", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "https://oglcnac.org/atlas/detail/Q14683", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs376589639", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376589639", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs376589639", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376589639", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs376589639", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376589639#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs376589639", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376589639", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IIDETMAQLQDLKNQHLAKK", "down_seq": "EVNDKNHEMEEIRKKLGGAN", "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": "Ser882", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q14683", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q14683" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "35008409", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35008409" }, { "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q14683", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q14683" } ] } ], "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "23", "chr_pos": "53396535", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S882", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs376589639", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376589639" }, { "id": "rs376589639", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs376589639" }, { "id": "rs376589639", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs376589639#frequency_tab" }, { "id": "rs376589639", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs376589639" } ], "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": "X", "chr_pos": "53396535", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S882", "disease": [ { "disease_id": "DOID:0080506", "recommended_name": { "id": "DOID:0080506", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080506", "name": "Cornelia de Lange syndrome 2", "description": "A Cornelia de Lange syndrome that has_material_basis_in a mutation in the SMC1A gene, which encodes a subunit of the cohesin complex, on chromosome Xp11." }, "synonyms": [ { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "An X-linked inherited form of Cornelia De Lange syndrome caused by mutations in the SMC1A gene mapped to chromosome Xp11.22. Patients have a milder form of the syndrome compared to patients with the NIPBL gene mutation." }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia De Lange syndrome type 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome caused by mutation in SMC1A", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "SMC1A Cornelia de Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "X-linked Cornelia De Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "CDLS2", "description": "" }, { "id": "MIM:300590", "resource": "MIM", "url": "https://www.omim.org/entry/300590", "name": "Cornelia de Lange syndrome 2", "description": "Cornelia de Lange syndrome 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" }, { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q14683-1.895.895", "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": 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": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14683-1.957.957", "start_pos": 957, "end_pos": 957, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint.", "journal": "Genes & development", "date": "2002", "authors": "Yazdi PT, Wang Y, Zhao S, Patel N, Lee EY, Qin J", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" } ] }, { "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Involvement of the cohesin protein, Smc1, in Atm-dependent and independent responses to DNA damage.", "journal": "Genes & development", "date": "2002", "authors": "Kim ST, Xu B, Kastan MB", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376" } ] }, { "title": "The cohesin complex is required for the DNA damage-induced G2/M checkpoint in mammalian cells.", "journal": "The EMBO journal", "date": "2009-09-02", "authors": "Watrin Erwan, Peters Jan-Michael", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "19629043", "url": "https://glygen.org/publication/PubMed/19629043" } ] }, { "title": "Spatial organization of the mammalian genome surveillance machinery in response to DNA strand breaks.", "journal": "The Journal of cell biology", "date": "2006", "authors": "Bekker-Jensen S, Lukas C, Kitagawa R, Melander F, Kastan MB, Bartek J, Lukas J", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "16618811", "url": "https://glygen.org/publication/PubMed/16618811" } ] }, { "title": "Cohesin promotes the repair of ionizing radiation-induced DNA double-strand breaks in replicated chromatin.", "journal": "Nucleic acids research", "date": "2010", "authors": "Bauerschmidt C, Arrichiello C, Burdak-Rothkamm S, Woodcock M, Hill MA, Stevens DL, Rothkamm K", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "19906707", "url": "https://glygen.org/publication/PubMed/19906707" } ] }, { "title": "Blood-based detection of radiation exposure in humans based on novel phospho-Smc1 ELISA.", "journal": "Radiation research", "date": "2011", "authors": "Ivey RG, Moore HD, Voytovich UJ, Thienes CP, Lorentzen TD, Pogosova-Agadjanyan EL, Frayo S, Izaguirre VK, Lundberg SJ, Hedin L, Badiozamani KR, Hoofnagle AN, Stirewalt DL, Wang P, Georges GE, Gopal AK, Paulovich AG", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "21388270", "url": "https://glygen.org/publication/PubMed/21388270" } ] }, { "title": "SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins.", "journal": "Scientific reports", "date": "2015", "authors": "Mannini L, Cucco F, Quarantotti V, Amato C, Tinti M, Tana L, Frattini A, Delia D, Krantz ID, Jessberger R, Musio A", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "26673124", "url": "https://glygen.org/publication/PubMed/26673124" } ] }, { "title": "Phosphorylation of SMC1A promotes hepatocellular carcinoma cell proliferation and migration.", "journal": "International journal of biological sciences", "date": "2018", "authors": "Zhang Y, Yi F, Wang L, Wang Z, Zhang N, Wang Z, Li Z, Song X, Wei S, Cao L", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "29988990", "url": "https://glygen.org/publication/PubMed/29988990" } ] }, { "title": "Radiation-Induced Phosphorylation of Serine 360 of SMC1 in Human Peripheral Blood Mononuclear Cells.", "journal": "Radiation research", "date": "2019", "authors": "Park S, Park JH, Ryu SH, Yeom J, Ryu JW, Park EY, Choi KC, Heo SH, Kim KH, Ha CH, Chang SK, Lee SW", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "30702968", "url": "https://glygen.org/publication/PubMed/30702968" } ] }, { "title": "The deacetylation-phosphorylation regulation of SIRT2-SMC1A axis as a mechanism of antimitotic catastrophe in early tumorigenesis.", "journal": "Science advances", "date": "2021-02", "authors": "Yi Fei, Zhang Ying, Wang Zhijun, Wang Zhuo, Li Ziwei, Zhou Tingting, Xu Hongde, Liu Jingwei, Jiang Bo, Li Xiaoman, Wang Liang, Bai Ning, Guo Qiqiang, Guan Yi, Feng Yanling, Mao Zhiyong, Fan Guangjian, Zhang Shengping, Wang Chuangui, Cao Longyue, O'Rourke Brian P, Wang Yang, Wu Yanmei, Wu Boquan, You Shilong, Zhang Naijin, Guan Junlin, Song Xiaoyu, Sun Yingxian, Wei Shi, Cao Liu", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "33627431", "url": "https://glygen.org/publication/PubMed/33627431" } ] }, { "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": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "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": "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": "11877376", "url": "https://glygen.org/publication/PubMed/11877376", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q14683*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "19629043", "url": "https://glygen.org/publication/PubMed/19629043", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16618811", "url": "https://glygen.org/publication/PubMed/16618811", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19906707", "url": "https://glygen.org/publication/PubMed/19906707", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21388270", "url": "https://glygen.org/publication/PubMed/21388270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26673124", "url": "https://glygen.org/publication/PubMed/26673124", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29988990", "url": "https://glygen.org/publication/PubMed/29988990", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30702968", "url": "https://glygen.org/publication/PubMed/30702968", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33627431", "url": "https://glygen.org/publication/PubMed/33627431", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DIKLPLSKGTMDDISQEEGS", "down_seq": "QGEDSVSGSQRISSIYAREA", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Reduces phosphorylation and the S-phase checkpoint activation. Abolishes S-phase activation; when associated with A-966.", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13315-1", "kinase_gene_name": "ATM", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "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": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376" }, { "database": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" } ], "site_lbl": "Ser957" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by ATM", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "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": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "IntAct", "id": "Q14683", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q14683*" }, { "database": "PubMed", "id": "19629043", "url": "https://glygen.org/publication/PubMed/19629043" }, { "database": "PubMed", "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376" }, { "database": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" }, { "database": "PubMed", "id": "16618811", "url": "https://glygen.org/publication/PubMed/16618811" }, { "database": "PubMed", "id": "19906707", "url": "https://glygen.org/publication/PubMed/19906707" }, { "database": "PubMed", "id": "21388270", "url": "https://glygen.org/publication/PubMed/21388270" }, { "database": "PubMed", "id": "26673124", "url": "https://glygen.org/publication/PubMed/26673124" }, { "database": "PubMed", "id": "29988990", "url": "https://glygen.org/publication/PubMed/29988990" }, { "database": "PubMed", "id": "30702968", "url": "https://glygen.org/publication/PubMed/30702968" }, { "database": "PubMed", "id": "33627431", "url": "https://glygen.org/publication/PubMed/33627431" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ], "site_lbl": "Ser957" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q14683-1.973.973", "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": 17 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14683-1.966.966", "start_pos": 966, "end_pos": 966, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "SMC1 is a downstream effector in the ATM/NBS1 branch of the human S-phase checkpoint.", "journal": "Genes & development", "date": "2002", "authors": "Yazdi PT, Wang Y, Zhao S, Patel N, Lee EY, Qin J", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" } ] }, { "title": "MSH2 and ATR form a signaling module and regulate two branches of the damage response to DNA methylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2003", "authors": "Wang Y, Qin J", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "14657349", "url": "https://glygen.org/publication/PubMed/14657349" } ] }, { "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Identification of two distinct human SMC protein complexes involved in mitotic chromosome dynamics.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "1998", "authors": "Schmiesing JA, Ball AR Jr, Gregson HC, Alderton JM, Zhou S, Yokomori K", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "9789013", "url": "https://glygen.org/publication/PubMed/9789013" } ] }, { "title": "Involvement of the cohesin protein, Smc1, in Atm-dependent and independent responses to DNA damage.", "journal": "Genes & development", "date": "2002", "authors": "Kim ST, Xu B, Kastan MB", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376" } ] }, { "title": "Cohesin promotes the repair of ionizing radiation-induced DNA double-strand breaks in replicated chromatin.", "journal": "Nucleic acids research", "date": "2010", "authors": "Bauerschmidt C, Arrichiello C, Burdak-Rothkamm S, Woodcock M, Hill MA, Stevens DL, Rothkamm K", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "19906707", "url": "https://glygen.org/publication/PubMed/19906707" } ] }, { "title": "Cohesin phosphorylation and mobility of SMC1 at ionizing radiation-induced DNA double-strand breaks in human cells.", "journal": "Experimental cell research", "date": "2011", "authors": "Bauerschmidt C, Woodcock M, Stevens DL, Hill MA, Rothkamm K, Helleday T", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "21056556", "url": "https://glygen.org/publication/PubMed/21056556" } ] }, { "title": "Blood-based detection of radiation exposure in humans based on novel phospho-Smc1 ELISA.", "journal": "Radiation research", "date": "2011", "authors": "Ivey RG, Moore HD, Voytovich UJ, Thienes CP, Lorentzen TD, Pogosova-Agadjanyan EL, Frayo S, Izaguirre VK, Lundberg SJ, Hedin L, Badiozamani KR, Hoofnagle AN, Stirewalt DL, Wang P, Georges GE, Gopal AK, Paulovich AG", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "21388270", "url": "https://glygen.org/publication/PubMed/21388270" } ] }, { "title": "Phosphorylation of SMC1 by ATR is required for desferrioxamine (DFO)-induced apoptosis.", "journal": "Cell death & disease", "date": "2011", "authors": "So EY, Ausman M, Saeki T, Ouchi T", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "21390062", "url": "https://glygen.org/publication/PubMed/21390062" } ] }, { "title": "SMC1B is present in mammalian somatic cells and interacts with mitotic cohesin proteins.", "journal": "Scientific reports", "date": "2015", "authors": "Mannini L, Cucco F, Quarantotti V, Amato C, Tinti M, Tana L, Frattini A, Delia D, Krantz ID, Jessberger R, Musio A", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "26673124", "url": "https://glygen.org/publication/PubMed/26673124" } ] }, { "title": "Phosphorylation of SMC1A promotes hepatocellular carcinoma cell proliferation and migration.", "journal": "International journal of biological sciences", "date": "2018", "authors": "Zhang Y, Yi F, Wang L, Wang Z, Zhang N, Wang Z, Li Z, Song X, Wei S, Cao L", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "29988990", "url": "https://glygen.org/publication/PubMed/29988990" } ] }, { "title": "The deacetylation-phosphorylation regulation of SIRT2-SMC1A axis as a mechanism of antimitotic catastrophe in early tumorigenesis.", "journal": "Science advances", "date": "2021-02", "authors": "Yi Fei, Zhang Ying, Wang Zhijun, Wang Zhuo, Li Ziwei, Zhou Tingting, Xu Hongde, Liu Jingwei, Jiang Bo, Li Xiaoman, Wang Liang, Bai Ning, Guo Qiqiang, Guan Yi, Feng Yanling, Mao Zhiyong, Fan Guangjian, Zhang Shengping, Wang Chuangui, Cao Longyue, O'Rourke Brian P, Wang Yang, Wu Yanmei, Wu Boquan, You Shilong, Zhang Naijin, Guan Junlin, Song Xiaoyu, Sun Yingxian, Wei Shi, Cao Liu", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "33627431", "url": "https://glygen.org/publication/PubMed/33627431" } ] }, { "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "title": "Functional interaction of BRCA1/ATM-associated BAAT1 with the DNA-PK catalytic subunit.", "journal": "Experimental and therapeutic medicine", "date": "2011", "authors": "So EY, Ouchi T", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "22977523", "url": "https://glygen.org/publication/PubMed/22977523" } ] } ], "crossref": [ { "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14657349", "url": "https://glygen.org/publication/PubMed/14657349", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "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": "9789013", "url": "https://glygen.org/publication/PubMed/9789013", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19906707", "url": "https://glygen.org/publication/PubMed/19906707", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21056556", "url": "https://glygen.org/publication/PubMed/21056556", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21388270", "url": "https://glygen.org/publication/PubMed/21388270", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21390062", "url": "https://glygen.org/publication/PubMed/21390062", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26673124", "url": "https://glygen.org/publication/PubMed/26673124", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29988990", "url": "https://glygen.org/publication/PubMed/29988990", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33627431", "url": "https://glygen.org/publication/PubMed/33627431", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22977523", "url": "https://glygen.org/publication/PubMed/22977523", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TMDDISQEEGSSQGEDSVSG", "down_seq": "QRISSIYAREALIEIDYGDL", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Reduces phosphorylation and the S-phase checkpoint activation. Increases sensitivity to DNA methylation. Abolishes S-phase activation; when associated with A-957.", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" }, { "database": "PubMed", "id": "14657349", "url": "https://glygen.org/publication/PubMed/14657349" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13315-1", "kinase_gene_name": "ATM", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" }, { "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": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "9789013", "url": "https://glygen.org/publication/PubMed/9789013" }, { "database": "PubMed", "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376" } ], "site_lbl": "Ser966" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by ATM and ATR", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "11877376", "url": "https://glygen.org/publication/PubMed/11877376" }, { "database": "PubMed", "id": "11877377", "url": "https://glygen.org/publication/PubMed/11877377" }, { "database": "PubMed", "id": "19906707", "url": "https://glygen.org/publication/PubMed/19906707" }, { "database": "PubMed", "id": "21056556", "url": "https://glygen.org/publication/PubMed/21056556" }, { "database": "PubMed", "id": "21388270", "url": "https://glygen.org/publication/PubMed/21388270" }, { "database": "PubMed", "id": "21390062", "url": "https://glygen.org/publication/PubMed/21390062" }, { "database": "PubMed", "id": "26673124", "url": "https://glygen.org/publication/PubMed/26673124" }, { "database": "PubMed", "id": "29988990", "url": "https://glygen.org/publication/PubMed/29988990" }, { "database": "PubMed", "id": "33627431", "url": "https://glygen.org/publication/PubMed/33627431" }, { "database": "PubMed", "id": "14657349", "url": "https://glygen.org/publication/PubMed/14657349" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "22977523", "url": "https://glygen.org/publication/PubMed/22977523" } ], "site_lbl": "Ser966" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14683-1.973.973", "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": 17 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q14683-1.1114.1114", "start_pos": 1114, "end_pos": 1114, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "AQAFLGPENPEEPYLDGINY", "down_seq": "CVAPGKRFRPMDNLSGGEKT", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NYN->NYS).", "chr_id": "23", "chr_pos": "53382328", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1114", "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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q14683-1.1127.1127", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14683-1.1129.1129", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14683-1.1129.1129", "start_pos": 1129, "end_pos": 1129, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DGINYNCVAPGKRFRPMDNL", "down_seq": "GGEKTVAALALLFAIHSYKP", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLS->NLL).", "chr_id": "23", "chr_pos": "53382283", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1129", "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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q14683-1.1114.1114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14683-1.1127.1127", "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": "Q14683-1.1166.1166", "start_pos": 1166, "end_pos": 1166, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1556885810", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556885810", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1556885810", "url": "https://www.ensembl.org/id/rs1556885810", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SYKPAPFFVLDEIDAALDNT", "down_seq": "IGKVANYIKEQSTCNFQAIV", "snv": [ { "evidence": [ { "id": "rs1556885810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556885810" }, { "id": "rs1556885810", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1556885810" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "X", "chr_pos": "53381028", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1166", "disease": [ { "disease_id": "DOID:0080506", "recommended_name": { "id": "DOID:0080506", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080506", "name": "Cornelia de Lange syndrome 2", "description": "A Cornelia de Lange syndrome that has_material_basis_in a mutation in the SMC1A gene, which encodes a subunit of the cohesin complex, on chromosome Xp11." }, "synonyms": [ { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "An X-linked inherited form of Cornelia De Lange syndrome caused by mutations in the SMC1A gene mapped to chromosome Xp11.22. Patients have a milder form of the syndrome compared to patients with the NIPBL gene mutation." }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia De Lange syndrome type 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome caused by mutation in SMC1A", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "SMC1A Cornelia de Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "X-linked Cornelia De Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "CDLS2", "description": "" }, { "id": "MIM:300590", "resource": "MIM", "url": "https://www.omim.org/entry/300590", "name": "Cornelia de Lange syndrome 2", "description": "Cornelia de Lange syndrome 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" }, { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "rs1556885810", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1556885810" }, { "id": "rs1556885810", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1556885810" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTT).", "chr_id": "X", "chr_pos": "53381028", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1166", "disease": [ { "disease_id": "DOID:0080506", "recommended_name": { "id": "DOID:0080506", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080506", "name": "Cornelia de Lange syndrome 2", "description": "A Cornelia de Lange syndrome that has_material_basis_in a mutation in the SMC1A gene, which encodes a subunit of the cohesin complex, on chromosome Xp11." }, "synonyms": [ { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "An X-linked inherited form of Cornelia De Lange syndrome caused by mutations in the SMC1A gene mapped to chromosome Xp11.22. Patients have a milder form of the syndrome compared to patients with the NIPBL gene mutation." }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia De Lange syndrome type 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome caused by mutation in SMC1A", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "SMC1A Cornelia de Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "X-linked Cornelia De Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "CDLS2", "description": "" }, { "id": "MIM:300590", "resource": "MIM", "url": "https://www.omim.org/entry/300590", "name": "Cornelia de Lange syndrome 2", "description": "Cornelia de Lange syndrome 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" }, { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q14683-1.1168.1168", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14683-1.1168.1168", "start_pos": 1168, "end_pos": 1168, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KPAPFFVLDEIDAALDNTNI", "down_seq": "KVANYIKEQSTCNFQAIVIS", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIG->NIC).", "chr_id": "23", "chr_pos": "53381023", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G1168", "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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q14683-1.1166.1166", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q14683-1.1198.1198", "start_pos": 1198, "end_pos": 1198, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "STCNFQAIVISLKEEFYTKA", "down_seq": "SLIGVYPEQGDCVISKVLTF", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "53380646", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E1198", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.1219.1219", "start_pos": 1219, "end_pos": 1219, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1259383708", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259383708", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1259383708", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1259383708#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1259383708", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1259383708", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1259383708", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1259383708", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SLIGVYPEQGDCVISKVLTF", "down_seq": "LTKYPDANPNPNEQ", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" }, { "id": "rs1259383708", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1259383708" }, { "id": "rs1259383708", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1259383708#frequency_tab" }, { "id": "rs1259383708", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1259383708" }, { "id": "rs1259383708", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1259383708" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLT->NLT).", "chr_id": "23", "chr_pos": "53380150", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1219", "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:0080506", "recommended_name": { "id": "DOID:0080506", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0080506", "name": "Cornelia de Lange syndrome 2", "description": "A Cornelia de Lange syndrome that has_material_basis_in a mutation in the SMC1A gene, which encodes a subunit of the cohesin complex, on chromosome Xp11." }, "synonyms": [ { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "An X-linked inherited form of Cornelia De Lange syndrome caused by mutations in the SMC1A gene mapped to chromosome Xp11.22. Patients have a milder form of the syndrome compared to patients with the NIPBL gene mutation." }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia De Lange syndrome type 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "Cornelia de Lange syndrome caused by mutation in SMC1A", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "SMC1A Cornelia de Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "X-linked Cornelia De Lange syndrome", "description": "" }, { "id": "MONDO:0010370", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010370", "name": "CDLS2", "description": "" }, { "id": "MIM:300590", "resource": "MIM", "url": "https://www.omim.org/entry/300590", "name": "Cornelia de Lange syndrome 2", "description": "Cornelia de Lange syndrome 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" }, { "id": "0080506", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0080506" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "YDKRKKEMVKAEEDTQFNYH", "down_seq": "KKNIAAERKEAKQEKEEADR", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "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 (5).", "chr_id": "23", "chr_pos": "53413285", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R188", "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" } ] }, { "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: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.353.353", "start_pos": 353, "end_pos": 353, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MDELEKEMLSVEKARQEFEE", "down_seq": "MEEESQSQGRDLTLEENQVK", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "53412051", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R353", "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: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q14683-1.358.358", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14683-1.360.360", "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": "Q14683-1.426.426", "start_pos": 426, "end_pos": 426, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RLDLEERKKVETEAKIKQKL", "down_seq": "EIEENQKRIEKLEEYITTSK", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "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": "23", "chr_pos": "53409481", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R426", "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: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELNQVMEQLGDARIDRQESS", "down_seq": "QQRKAEIMESIKRLYPGSVY", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "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": "23", "chr_pos": "53409120", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R496", "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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.599.599", "start_pos": 599, "end_pos": 599, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KPTDEKLRELKGAKLVIDVI", "down_seq": "YEPPHIKKALQYACGNALVC", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "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": "23", "chr_pos": "53405609", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R599", "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: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.711.711", "start_pos": 711, "end_pos": 711, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AKRKEAELRQVQSQAHGLQM", "down_seq": "LKYSQSDLEQTKTRHLALNL", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "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 (4).", "chr_id": "23", "chr_pos": "53405077", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R711", "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: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q14683-1.722.722", "categories": [ "glycosylation_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": "Q14683-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VKTLRDLIHGAPVGKPAANR", "down_seq": "FVSMVYSEEGAEDRTFARVI", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRA->NRT).", "chr_id": "23", "chr_pos": "53415047", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A78", "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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.790.790", "start_pos": 790, "end_pos": 790, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NQVEDEVFEEFCREIGVRNI", "down_seq": "EFEEEKVKRQNEIAKKRLEF", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "53403617", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R790", "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: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": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.895.895", "start_pos": 895, "end_pos": 895, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NQHLAKKSEVNDKNHEMEEI", "down_seq": "KKLGGANKEMTHLQKEVTAI", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "53396497", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R895", "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: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14683-1.882.882", "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": "Q14683-1.960.960", "start_pos": 960, "end_pos": 960, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q14683", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LPLSKGTMDDISQEEGSSQG", "down_seq": "DSVSGSQRISSIYAREALIE", "snv": [ { "evidence": [ { "id": "Q14683", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q14683" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "53394872", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "E960", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID: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": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14683-1.973.973", "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": "Q14683-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "EIENFKSYKGRQIIGPFQRF", "down_seq": "AIIGPNGSGKSNLMDAISFV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr28" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.358.358", "start_pos": 358, "end_pos": 358, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] }, { "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "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": "KEMLSVEKARQEFEERMEEE", "down_seq": "QSQGRDLTLEENQVKKYHRL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser358" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q14683-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14683-1.360.360", "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": "Q14683-1.360.360", "start_pos": 360, "end_pos": 360, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] }, { "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] }, { "title": "Radiation-Induced Phosphorylation of Serine 360 of SMC1 in Human Peripheral Blood Mononuclear Cells.", "journal": "Radiation research", "date": "2019", "authors": "Park S, Park JH, Ryu SH, Yeom J, Ryu JW, Park EY, Choi KC, Heo SH, Kim KH, Ha CH, Chang SK, Lee SW", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "30702968", "url": "https://glygen.org/publication/PubMed/30702968" } ] } ], "crossref": [ { "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683", "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": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30702968", "url": "https://glygen.org/publication/PubMed/30702968", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MLSVEKARQEFEERMEEESQ", "down_seq": "QGRDLTLEENQVKKYHRLKE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "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": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" }, { "database": "PubMed", "id": "30702968", "url": "https://glygen.org/publication/PubMed/30702968" } ], "site_lbl": "Ser360" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q14683-1.353.353", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14683-1.358.358", "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": "Q14683-1.841.841", "start_pos": 841, "end_pos": 841, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "LDFEKNQLKEDQDKVHMWEQ", "down_seq": "VKKDENEIEKLKKEEQRHMK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ], "site_lbl": "Thr841" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "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": "Q14683-1.951.951", "start_pos": 951, "end_pos": 951, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "QACKMQDIKLPLSKGTMDDI", "down_seq": "QEEGSSQGEDSVSGSQRISS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ], "site_lbl": "Ser951" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q14683-1.971.971", "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": "Q14683-1.956.956", "start_pos": 956, "end_pos": 956, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QDIKLPLSKGTMDDISQEEG", "down_seq": "SQGEDSVSGSQRISSIYARE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser956" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q14683-1.973.973", "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": "Q14683-1.962.962", "start_pos": 962, "end_pos": 962, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSKGTMDDISQEEGSSQGED", "down_seq": "VSGSQRISSIYAREALIEID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "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": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser962" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q14683-1.973.973", "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": "Q14683-1.964.964", "start_pos": 964, "end_pos": 964, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "KGTMDDISQEEGSSQGEDSV", "down_seq": "GSQRISSIYAREALIEIDYG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser964" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q14683-1.973.973", "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": "Q14683-1.970.970", "start_pos": 970, "end_pos": 970, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "database": "iPTMnet", "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": "ISQEEGSSQGEDSVSGSQRI", "down_seq": "SIYAREALIEIDYGDLCEDL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "19691289", "url": "https://glygen.org/publication/PubMed/19691289" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser970" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q14683-1.971.971", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q14683-1.973.973", "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": "Q14683-1.971.971", "start_pos": 971, "end_pos": 971, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "SQEEGSSQGEDSVSGSQRIS", "down_seq": "IYAREALIEIDYGDLCEDLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser971" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q14683-1.951.951", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q14683-1.973.973", "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": "Q14683-1.973.973", "start_pos": 973, "end_pos": 973, "uniprot_canonical_ac": "Q14683-1", "length": 1233, "uniprot_id": "SMC1A_HUMAN", "protein_name": "Structural maintenance of chromosomes protein 1A", "refseq_ac": "NP_006297", "refseq_name": "structural maintenance of chromosomes protein 1A isoform 1", "gene_name": "SMC1A", "gene_names_uniprotkb": "SMC1A; DXS423E; KIAA0178; SB1.8; SMC1L1; SMC1", "gene_names_refseq": "CDLS2; DEE85; DXS423E; EIEE85; SB1.8; SMC1A; SMC1L1; SMC1alpha; SMC1; SMCB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" } ], "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": "Q14683", "url": "https://www.uniprot.org/uniprotkb/Q14683" }, { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683", "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": "EEGSSQGEDSVSGSQRISSI", "down_seq": "AREALIEIDYGDLCEDLKDA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q14683", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q14683" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr973" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "882", "end_pos": "882" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "957", "end_pos": "957" }, { "start_pos": "966", "end_pos": "966" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1114", "end_pos": "1114" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "1166", "end_pos": "1166" }, { "start_pos": "1168", "end_pos": "1168" }, { "start_pos": "1198", "end_pos": "1198" }, { "start_pos": "1219", "end_pos": "1219" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "426", "end_pos": "426" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "549", "end_pos": "549" }, { "start_pos": "599", "end_pos": "599" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "882", "end_pos": "882" }, { "start_pos": "895", "end_pos": "895" }, { "start_pos": "960", "end_pos": "960" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "28", "end_pos": "28" }, { "start_pos": "358", "end_pos": "358" }, { "start_pos": "360", "end_pos": "360" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "841", "end_pos": "841" }, { "start_pos": "951", "end_pos": "951" }, { "start_pos": "956", "end_pos": "956" }, { "start_pos": "957", "end_pos": "957" }, { "start_pos": "962", "end_pos": "962" }, { "start_pos": "964", "end_pos": "964" }, { "start_pos": "966", "end_pos": "966" }, { "start_pos": "970", "end_pos": "970" }, { "start_pos": "971", "end_pos": "971" }, { "start_pos": "973", "end_pos": "973" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q14683-1.956.956", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q14683-1.957.957", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q14683-1.960.960", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q14683-1.962.962", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q14683-1.964.964", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q14683-1.966.966", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q14683-1.970.970", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q14683-1.971.971", "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": "O95197-1.234.234", "start_pos": 234, "end_pos": 234, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs755612658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755612658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755612658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755612658", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755612658", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755612658", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs955012279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955012279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs955012279", "url": "https://www.ensembl.org/id/rs955012279", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs755612658", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs755612658", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PTEYSKVEGIYTYSLSPSKV", "down_seq": "GDDVIEKDSPESPFEVIIDK", "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": "Ser234", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95197", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "snv": [ { "evidence": [ { "id": "rs755612658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755612658" }, { "id": "rs755612658", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755612658" }, { "id": "rs755612658", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755612658" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "11", "chr_pos": "63719203", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S234", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs955012279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955012279" }, { "id": "rs955012279", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs955012279" } ], "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": "11", "chr_pos": "63719202", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S234", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" }, { "id": "rs755612658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755612658" }, { "id": "rs755612658", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755612658" }, { "id": "rs755612658", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755612658" }, { "id": "rs755612658", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs755612658" } ], "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: o-glyco-site-loss (S->L).", "chr_id": "11", "chr_pos": "63719203", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S234", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O95197-1.229.229", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O95197-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O95197-1.246.246", "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": 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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95197-1.391.391", "start_pos": 391, "end_pos": 391, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NSEIPVVNLKTSTHQKTPVC", "down_seq": "IDGSTPITKSTGDWAEASLQ", "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": "Ser391", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95197", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "O95197", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95197" } ] } ], "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "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": "11", "chr_pos": "63719674", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S391", "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": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2670", "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": "11", "chr_pos": "63719674", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S391", "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": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O95197-1.396.396", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O95197-1.399.399", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95197-1.396.396", "start_pos": 396, "end_pos": 396, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1210458133", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1210458133", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1210458133", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1210458133", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VVNLKTSTHQKTPVCSIDGS", "down_seq": "PITKSTGDWAEASLQQENAI", "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": "Thr396", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95197", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "snv": [ { "evidence": [ { "id": "rs1210458133", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1210458133" }, { "id": "rs1210458133", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1210458133" } ], "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": "11", "chr_pos": "63719688", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T396", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O95197-1.391.391", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O95197-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O95197-1.416.416", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95197-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2011616616", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2011616616", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2011616616", "url": "https://www.ensembl.org/id/rs2011616616", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LKTSTHQKTPVCSIDGSTPI", "down_seq": "KSTGDWAEASLQQENAITGK", "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": "Thr399", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95197", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "O95197", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95197" } ] } ], "snv": [ { "evidence": [ { "id": "rs2011616616", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2011616616" }, { "id": "rs2011616616", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2011616616" } ], "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": "63719698", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T399", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O95197-1.391.391", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O95197-1.396.396", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O95197-1.416.416", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95197-1.526.526", "start_pos": 526, "end_pos": 526, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs540444457", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540444457", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs540444457", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540444457#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs540444457", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540444457", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EDITADTSFENNKIQAEKPV", "down_seq": "IPSAVVKTGEREIKEIPSCE", "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": "Ser526", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95197", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "O95197", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95197" } ] } ], "snv": [ { "evidence": [ { "id": "rs540444457", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs540444457" }, { "id": "rs540444457", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs540444457#frequency_tab" }, { "id": "rs540444457", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs540444457" } ], "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": "11", "chr_pos": "63720079", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S526", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O95197-1.511.511", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95197-1.678.678", "start_pos": 678, "end_pos": 678, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "database": "O-GlcNAc Atlas", "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] } ], "crossref": [ { "id": "33465208", "url": "https://glygen.org/publication/PubMed/33465208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "https://oglcnac.org/atlas/detail/O95197", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FTETRDKGIVDSERNAFKAI", "down_seq": "EKMTDFKTTPPVEVLHENES", "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": "Ser678", "evidence": [ { "id": "33465208", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33465208" }, { "id": "O95197", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O95197" }, { "id": "28657654", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28657654" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "O95197", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O95197" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O95197-1.668.668", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O95197-1.728.728", "start_pos": 728, "end_pos": 728, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "SKYSEQSKETNGSEPLGVFP", "down_seq": "QGTPVASLDLEQEQLTIKAL", "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": "Thr728", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "O95197-1.735.735", "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": "O95197-1.1008.1008", "start_pos": 1008, "end_pos": 1008, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FSVPIVYEKYKTQIDHYVGI", "down_seq": "RDQTKSIVEKIQAKLPGIAK", "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "glycoeffect": [], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "63756139", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A1008", "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: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": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KAAFDKEFKDSYKESTDDFG", "down_seq": "WSVHTDKESSEDISETNDKL", "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "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 (SWS->NWS).", "chr_id": "11", "chr_pos": "63719323", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S274", "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": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "O95197-1.283.283", "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": "O95197-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs371391643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371391643", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs371391643", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371391643", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs371391643", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371391643#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs371391643", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371391643", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "SRQFSHTNAALEEVSRCVND", "down_seq": "HNFTNEILTWDLVPQVKQQT", "snv": [ { "evidence": [ { "id": "rs371391643", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371391643" }, { "id": "rs371391643", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs371391643" }, { "id": "rs371391643", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs371391643#frequency_tab" }, { "id": "rs371391643", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs371391643" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDM->NDT).", "chr_id": "11", "chr_pos": "63719497", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M332", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O95197-1.316.316", "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": "O95197-1.353.353", "start_pos": 353, "end_pos": 353, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1331241032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1331241032", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1331241032", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1331241032#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1331241032", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1331241032", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HNFTNEILTWDLVPQVKQQT", "down_seq": "KSSDCITKTTGLDMSEYNSE", "snv": [ { "evidence": [ { "id": "rs1331241032", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1331241032" }, { "id": "rs1331241032", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1331241032#frequency_tab" }, { "id": "rs1331241032", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1331241032" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DKS->NKS).", "chr_id": "11", "chr_pos": "63719559", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D353", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "O95197-1.366.366", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.366.366", "start_pos": 366, "end_pos": 366, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs150901896", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150901896", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150901896", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150901896", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150901896", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150901896#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150901896", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150901896", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PQVKQQTDKSSDCITKTTGL", "down_seq": "MSEYNSEIPVVNLKTSTHQK", "snv": [ { "evidence": [ { "id": "rs150901896", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150901896" }, { "id": "rs150901896", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150901896" }, { "id": "rs150901896", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150901896#frequency_tab" }, { "id": "rs150901896", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150901896" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DMS->NMS).", "chr_id": "11", "chr_pos": "63719598", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D366", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O95197-1.353.353", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1941062360", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1941062360", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1941062360", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1941062360#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AEPSAPGGGGSPGACPALGT", "down_seq": "SCSSSCADSFVSSSSSQPVS", "snv": [ { "evidence": [ { "id": "rs1941062360", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1941062360" }, { "id": "rs1941062360", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1941062360#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KSC->NSC).", "chr_id": "11", "chr_pos": "63681756", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K40", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O95197-1.30.30", "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": "O95197-1.416.416", "start_pos": 416, "end_pos": 416, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1323524050", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1323524050", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1323524050", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1323524050#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TPITKSTGDWAEASLQQENA", "down_seq": "TGKPVPDSLNSTKEFSIKGV", "snv": [ { "evidence": [ { "id": "rs1323524050", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1323524050" }, { "id": "rs1323524050", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1323524050#frequency_tab" } ], "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": "11", "chr_pos": "63719749", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I416", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O95197-1.396.396", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "O95197-1.399.399", "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": "O95197-1.511.511", "start_pos": 511, "end_pos": 511, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1347911885", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347911885", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1347911885", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347911885", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ITEADSSGESDDTVIEDITA", "down_seq": "TSFENNKIQAEKPVSIPSAV", "snv": [ { "evidence": [ { "id": "rs1347911885", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1347911885" }, { "id": "rs1347911885", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1347911885" } ], "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": "11", "chr_pos": "63720033", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D511", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "O95197-1.526.526", "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": "O95197-1.594.594", "start_pos": 594, "end_pos": 594, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RSPASEAACSKVPDTNVSLE", "down_seq": "VSEVAPEKPITTENPKLPST", "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "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 (DVS->NVS).", "chr_id": "11", "chr_pos": "63720282", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D594", "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": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.668.668", "start_pos": 668, "end_pos": 668, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DSSPEDLIAAFTETRDKGIV", "down_seq": "SERNAFKAISEKMTDFKTTP", "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "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": "63720504", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D668", "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": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O95197-1.649.649", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "O95197-1.650.650", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O95197-1.678.678", "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": "O95197-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MAEPS", "down_seq": "ATQSHSISSSSFGAEPSAPG", "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "A", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "11", "chr_pos": "63681653", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A6", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.706.706", "start_pos": 706, "end_pos": 706, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1013173070", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1013173070", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1013173070", "url": "https://www.ensembl.org/id/rs1013173070", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TTPPVEVLHENESGGSEIKD", "down_seq": "GSKYSEQSKETNGSEPLGVF", "snv": [ { "evidence": [ { "id": "rs1013173070", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1013173070" }, { "id": "rs1013173070", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1013173070" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IGS->NGS).", "chr_id": "11", "chr_pos": "63720619", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I706", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.758.758", "start_pos": 758, "end_pos": 758, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1198370030", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1198370030", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1198370030", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1198370030#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LEQEQLTIKALKELGERQVE", "down_seq": "STSAQRDAELPSEEVLKQTF", "snv": [ { "evidence": [ { "id": "rs1198370030", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1198370030" }, { "id": "rs1198370030", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1198370030#frequency_tab" } ], "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": "11", "chr_pos": "63720776", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K758", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.919.919", "start_pos": 919, "end_pos": 919, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1450820876", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450820876", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1450820876", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1450820876#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1450820876", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1450820876", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VIQAVQKSEEGHPFKAYLDV", "down_seq": "ITLSSEAFHNYMNAAMVHIN", "snv": [ { "evidence": [ { "id": "rs1450820876", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1450820876" }, { "id": "rs1450820876", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1450820876#frequency_tab" }, { "id": "rs1450820876", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1450820876" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DIT->NIT).", "chr_id": "11", "chr_pos": "63752523", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D919", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "O95197-1.934.934", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.934.934", "start_pos": 934, "end_pos": 934, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1237447467", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237447467", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1237447467", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237447467", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AYLDVDITLSSEAFHNYMNA", "down_seq": "MVHINRALKLIIRLFLVEDL", "snv": [ { "evidence": [ { "id": "rs1237447467", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1237447467" }, { "id": "rs1237447467", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1237447467" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAA->NAT).", "chr_id": "11", "chr_pos": "63752568", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A934", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O95197-1.919.919", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O95197-1.941.941", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O95197-1.947.947", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.941.941", "start_pos": 941, "end_pos": 941, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1211971903", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1211971903", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1211971903", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1211971903#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1211971903", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1211971903", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TLSSEAFHNYMNAAMVHINR", "down_seq": "LKLIIRLFLVEDLVDSLKLA", "snv": [ { "evidence": [ { "id": "rs1211971903", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1211971903" }, { "id": "rs1211971903", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1211971903#frequency_tab" }, { "id": "rs1211971903", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1211971903" } ], "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": "11", "chr_pos": "63752589", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A941", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O95197-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O95197-1.947.947", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.947.947", "start_pos": 947, "end_pos": 947, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FHNYMNAAMVHINRALKLII", "down_seq": "LFLVEDLVDSLKLAVFMWLM", "snv": [ { "evidence": [ { "id": "O95197", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O95197" } ], "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": "63752607", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R947", "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": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O95197-1.934.934", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O95197-1.941.941", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2011546087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2011546087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2011546087", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2011546087#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2011546087", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2011546087", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EPSSEIMTSSFLSSSEIHNT", "down_seq": "LTILHGEKSHVLGSQPILAK", "snv": [ { "evidence": [ { "id": "rs2011546087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2011546087" }, { "id": "rs2011546087", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2011546087#frequency_tab" }, { "id": "rs2011546087", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2011546087" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTG->NTS).", "chr_id": "11", "chr_pos": "63718788", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G96", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAQKPPTEYSKVEGIYTYSL", "down_seq": "PSKVSGDDVIEKDSPESPFE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser229" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O95197-1.234.234", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O95197-1.243.243", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O95197-1.246.246", "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": "O95197-1.243.243", "start_pos": 243, "end_pos": 243, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYTYSLSPSKVSGDDVIEKD", "down_seq": "PESPFEVIIDKAAFDKEFKD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "site_lbl": "Ser243" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O95197-1.229.229", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O95197-1.234.234", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O95197-1.246.246", "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": "O95197-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YSLSPSKVSGDDVIEKDSPE", "down_seq": "PFEVIIDKAAFDKEFKDSYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser246" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O95197-1.229.229", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O95197-1.234.234", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O95197-1.243.243", "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": "O95197-1.283.283", "start_pos": 283, "end_pos": 283, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DSYKESTDDFGSWSVHTDKE", "down_seq": "SEDISETNDKLFPLRNKEAG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "site_lbl": "Ser283" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O95197-1.274.274", "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": 0 } ], "sort_fields": [] } ] }, { "id": "O95197-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SHSISSSSFGAEPSAPGGGG", "down_seq": "PGACPALGTKSCSSSCADSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser30" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "O95197-1.40.40", "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": "O95197-1.316.316", "start_pos": 316, "end_pos": 316, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PLRNKEAGRYPMSALLSRQF", "down_seq": "HTNAALEEVSRCVNDMHNFT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser316" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "O95197-1.332.332", "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": "O95197-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IKGVQGNMQKQDDTLAELPG", "down_seq": "PPEKCDSLGSGVATVKVVLP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser453" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "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": "O95197-1.649.649", "start_pos": 649, "end_pos": 649, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VTTSAYLESLHGKNVKHIDD", "down_seq": "SPEDLIAAFTETRDKGIVDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser649" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "O95197-1.650.650", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O95197-1.668.668", "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": "O95197-1.650.650", "start_pos": 650, "end_pos": 650, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "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": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTSAYLESLHGKNVKHIDDS", "down_seq": "PEDLIAAFTETRDKGIVDSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O95197", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O95197" } ], "site_lbl": "Ser650" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "O95197-1.649.649", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O95197-1.668.668", "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": "O95197-1.735.735", "start_pos": 735, "end_pos": 735, "uniprot_canonical_ac": "O95197-1", "length": 1032, "uniprot_id": "RTN3_HUMAN", "protein_name": "Reticulon-3", "refseq_ac": "NP_001252518", "refseq_name": "reticulon-3 isoform e", "gene_name": "RTN3", "gene_names_uniprotkb": "RTN3; ASYIP; NSPL2", "gene_names_refseq": "ASYIP; HAP; NSPL2; NSPLII; RTN3-A1; RTN3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KETNGSEPLGVFPTQGTPVA", "down_seq": "LDLEQEQLTIKALKELGERQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O95197", "url": "https://www.uniprot.org/uniprotkb/O95197" } ], "site_lbl": "Ser735" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "234", "end_pos": "234" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "678", "end_pos": "678" }, { "start_pos": "728", "end_pos": "728" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1008", "end_pos": "1008" }, { "start_pos": "234", "end_pos": "234" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "353", "end_pos": "353" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "391", "end_pos": "391" }, { "start_pos": "396", "end_pos": "396" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "416", "end_pos": "416" }, { "start_pos": "511", "end_pos": "511" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "594", "end_pos": "594" }, { "start_pos": "668", "end_pos": "668" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "706", "end_pos": "706" }, { "start_pos": "758", "end_pos": "758" }, { "start_pos": "919", "end_pos": "919" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "947", "end_pos": "947" }, { "start_pos": "96", "end_pos": "96" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "229", "end_pos": "229" }, { "start_pos": "243", "end_pos": "243" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "283", "end_pos": "283" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "316", "end_pos": "316" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "650", "end_pos": "650" }, { "start_pos": "735", "end_pos": "735" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O95197-1.728.728", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.103.103", "start_pos": 103, "end_pos": 103, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "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": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Enrichment of glycopeptides for glycan structure and attachment site identification.", "journal": "Nature methods", "date": "2009", "authors": "Nilsson J, Ruetschi U, Halim A, Hesse C, Carlsohn E, Brinkmalm G, Larson G", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" }, { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "19838169", "url": "https://glygen.org/publication/PubMed/19838169" } ] }, { "title": "Distinct urinary glycoprotein signatures in prostate cancer patients.", "journal": "Oncotarget", "date": "2018", "authors": "Kawahara R, Ortega F, Rosa-Fernandes L, Guimaraes V, Quina D, Nahas W, Schwammle V, Srougi M, Leite KRM, Thaysen-Andersen M, Larsen MR, Palmisano G", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853" } ] }, { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] }, { "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": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Structural basis for complement factor I control and its disease-associated sequence polymorphisms.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Roversi P, Johnson S, Caesar JJ, McLean F, Leath KJ, Tsiftsoglou SA, Morgan BP, Harris CL, Sim RB, Lea SM", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352" } ] }, { "title": "A strategy for precise and large scale identification of core fucosylated glycoproteins.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Jia W, Lu Z, Fu Y, Wang HP, Wang LH, Chi H, Yuan ZF, Zheng ZB, Song LN, Han HH, Liang YM, Wang JL, Cai Y, Zhang YK, Deng YL, Ying WT, He SM, Qian XH", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "19139490", "url": "https://glygen.org/publication/PubMed/19139490" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] }, { "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": "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": "P05156@N103", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N103", "database": "GPTwiki", "categories": [ "Other" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19838169", "url": "https://glygen.org/publication/PubMed/19838169", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "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": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19139490", "url": "https://glygen.org/publication/PubMed/19139490", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2XRC", "url": "https://www.rcsb.org/structure/2XRC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "5O32", "url": "https://www.rcsb.org/structure/5O32", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2XRC|D|85", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|C|85", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|B|85", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|A|85", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|H|103", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|D|103", "url": "", "database": "", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PTYCQQKSLECLHPGTKFLN", "down_seq": "GTCTAEGKFSVSLKHGNTDS", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "P05156@N103", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N103" }, { "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": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G04854VP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G06247RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G11911BT", "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": "Asn103", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G22140GZ", "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": "Asn103", "evidence": [ { "id": "19838169", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19838169" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G26330YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G27126ED", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G28681TP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G37399XV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G40574BA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G46503DX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "30237853", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30237853" }, { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "glytoucan_ac": "G50045TK", "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": "Asn103", "evidence": [ { "id": "19838169", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19838169" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G51653BI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G52527GH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "FLNnGTCTAEGK", "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": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G66538GV", "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": "Asn103", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G72790NZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNNGTCTAEGK", "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": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G86182NS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G90659AW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "G92050GC", "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": "Asn103", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "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": "G95865ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FLNnGTCTAEGK", "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": "Complex", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) (complex) asparagine;Complex", "icn3d_view": { "label": "iCn3D", "url": "https://www.ncbi.nlm.nih.gov/Structure/icn3d/?bcifid=2XRC&bu=0&command=select+.D:85;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn103", "evidence": [ { "id": "P05156", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "id": "19838169", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19838169" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "21768352", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21768352" }, { "id": "19139490", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19139490" }, { "id": "2XRC", "database": "PDB", "url": "https://www.rcsb.org/sequence/2XRC" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "5O32", "database": "PDB", "url": "https://www.rcsb.org/structure/5O32" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P05156-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05156-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P05156-1.113.113", "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": 42 }, { "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": 41 }, { "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": 41 } ], "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": 41 }, { "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": 41 }, { "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": 41 } ], "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05156-1.177.177", "start_pos": 177, "end_pos": 177, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "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": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes.", "journal": "Journal of proteome research", "date": "2020", "authors": "Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Heck AJR", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "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": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "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" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Structural basis for complement factor I control and its disease-associated sequence polymorphisms.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Roversi P, Johnson S, Caesar JJ, McLean F, Leath KJ, Tsiftsoglou SA, Morgan BP, Harris CL, Sim RB, Lea SM", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352" } ] }, { "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": "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": "P05156@N177", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N177", "database": "GPTwiki", "categories": [ "Other" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "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": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2XRC", "url": "https://www.rcsb.org/structure/2XRC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "5O32", "url": "https://www.rcsb.org/structure/5O32", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2XRC|B|159", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|A|159", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|H|177", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|D|177", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs753060374", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753060374", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753060374", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753060374", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753060374", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753060374#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753060374", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753060374", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LGFQQGADTQRRFKLSDLSI", "down_seq": "STECLHVHCRGLETSLAECT", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "P05156@N177", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N177" }, { "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": "G04854VP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G06247RL", "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": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "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": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "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": "Asn177", "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": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G15169WU", "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": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G15664MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G22310AV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "glytoucan_ac": "G23863VK", "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": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G43669FQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G45495MK", "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": "Asn177", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G47518TP", "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": "Asn177", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "glytoucan_ac": "G50045TK", "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": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G52527GH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G56518TU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "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": "G61256FT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G77669RF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "LSDLSINSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G83555HU", "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": "Asn177", "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": "Asn177", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G85144OK", "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": "Asn177", "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": "G88374WZ", "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": "Asn177", "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": "G92551JA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G94470IW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LSDLSInSTECLHVHCR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "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": "G94917XT", "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": "Asn177", "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": "", "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=2XRC&bu=0&command=select+.B:159;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn177", "evidence": [ { "id": "P05156", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "21768352", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21768352" }, { "id": "2XRC", "database": "PDB", "url": "https://www.rcsb.org/sequence/2XRC" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "5O32", "database": "PDB", "url": "https://www.rcsb.org/structure/5O32" } ] } ], "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->HST).", "chr_id": "4", "chr_pos": "109761646", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N177", "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": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" }, { "id": "rs753060374", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753060374" }, { "id": "rs753060374", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753060374" }, { "id": "rs753060374", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753060374#frequency_tab" }, { "id": "rs753060374", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753060374" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->IST).", "chr_id": "4", "chr_pos": "109761645", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N177", "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:0110025", "recommended_name": { "id": "DOID:0110025", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110025", "name": "age related macular degeneration 13", "description": "An age related macular degeneration conferred by heterozygous mutation in the CFI gene on chromosome 4q25." }, "synonyms": [ { "id": "DOID:0110025", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110025", "name": "ARMD13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "age related macular degeneration 13", "description": "An inherited susceptibility or predisposition to developing age related macular degeneration in which the cause of the disease is a mutation in the CFI gene." }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "ARMD13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "CFI age-related macular degeneration", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "age related macular degeneration type 13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "age-related macular degeneration caused by mutation in CFI", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "macular degeneration, age-related, 13, susceptibility to", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "macular degeneration, age-related, type 13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "macular degeneration, age-related, 13", "description": "" }, { "id": "MIM:615439", "resource": "MIM", "url": "https://www.omim.org/entry/615439", "name": "Macular degeneration, age-related, 13", "description": "Macular degeneration, age-related, 13" } ], "unlinked_id_list": [], "evidence": [ { "id": "615439", "database": "MIM", "url": "https://www.omim.org/entry/615439" }, { "id": "0110025", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110025" } ] }, { "disease_id": "DOID:0050419", "recommended_name": { "id": "DOID:0050419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050419", "name": "complement factor I deficiency", "description": "A complement deficiency that is characterized by recurrent pyogenic bacterial infections that is the result of complement component 3 deficiency." }, "synonyms": [ { "id": "DOID:0050419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050419", "name": "C3 INACTIVATOR DEFICIENCY", "description": "" }, { "id": "DOID:0050419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050419", "name": "COMPLEMENT COMPONENT 3 INACTIVATOR DEFICIENCY", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "complement factor I deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "C3 inactivator deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "complement component 3 inactivator deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "complement factor I deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "CFID", "description": "" }, { "id": "MIM:610984", "resource": "MIM", "url": "https://www.omim.org/entry/610984", "name": "Complement factor I deficiency", "description": "Complement factor I deficiency" } ], "unlinked_id_list": [], "evidence": [ { "id": "610984", "database": "MIM", "url": "https://www.omim.org/entry/610984" }, { "id": "0050419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0050419" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P05156-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05156-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05156-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05156-1.197.197", "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": 41 }, { "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": 40 }, { "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": 40 } ], "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": 40 }, { "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": 40 }, { "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": 40 } ], "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05156-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "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": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "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" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "title": "Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis.", "journal": "Nature methods", "date": "2021", "authors": "Kawahara R, Chernykh A, Alagesan K, Bern M, Cao W, Chalkley RJ, Cheng K, Choo MS, Edwards N, Goldman R, Hoffmann M, Hu Y, Huang Y, Kim JY, Kletter D, Liquet B, Liu M, Mechref Y, Meng B, Neelamegham S, Nguyen-Khuong T, Nilsson J, Pap A, Park GW, Parker BL, Pegg CL, Penninger JM, Phung TK, Pioch M, Rapp E, Sakalli E, Sanda M, Schulz BL, Scott NE, Sofronov G, Stadlmann J, Vakhrushev SY, Woo CM, Wu HY, Yang P, Ying W, Zhang H, Zhang Y, Zhao J, Zaia J, Haslam SM, Palmisano G, Yoo JS, Larson G, Khoo KH, Medzihradszky KF, Kolarich D, Packer NH, Thaysen-Andersen M", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "34725484", "url": "https://glygen.org/publication/PubMed/34725484" } ] }, { "title": "Screening for N-glycosylated proteins by liquid chromatography mass spectrometry.", "journal": "Proteomics", "date": "2004", "authors": "Bunkenborg J, Pilch BJ, Podtelejnikov AV, Wisniewski JR", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "14760718", "url": "https://glygen.org/publication/PubMed/14760718" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Structural basis for complement factor I control and its disease-associated sequence polymorphisms.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Roversi P, Johnson S, Caesar JJ, McLean F, Leath KJ, Tsiftsoglou SA, Morgan BP, Harris CL, Sim RB, Lea SM", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352" } ] }, { "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": "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": "P05156@N464", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N464", "database": "GPTwiki", "categories": [ "Other" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742", "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": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725484", "url": "https://glygen.org/publication/PubMed/34725484", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "14760718", "url": "https://glygen.org/publication/PubMed/14760718", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2XRC", "url": "https://www.rcsb.org/structure/2XRC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "5O32", "url": "https://www.rcsb.org/structure/5O32", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2XRC|D|446", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|C|446", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|B|446", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|A|446", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|J|464", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|I|464", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs759927335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759927335", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759927335", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759927335", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759927335", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759927335#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759927335", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759927335", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CELPRSIPACVPWSPYLFQP", "down_seq": "DTCIVSGWGREKDNERVFSL", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "P05156@N464", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N464" }, { "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": "G04854VP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G06247RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G10846ZT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G26330YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G31986NC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G37995HC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPNDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G40574BA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" }, { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "34725484", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725484" } ] }, { "glytoucan_ac": "G51653BI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G72747WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "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": "Asn464", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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": "G94470IW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SIPACVPWSPYLFQPnDTCIVSGWGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "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=2XRC&bu=0&command=select+.D:446;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn464", "evidence": [ { "id": "P05156", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "id": "14760718", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/14760718" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "21768352", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21768352" }, { "id": "2XRC", "database": "PDB", "url": "https://www.rcsb.org/sequence/2XRC" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "5O32", "database": "PDB", "url": "https://www.rcsb.org/structure/5O32" } ] } ], "snv": [ { "evidence": [ { "id": "rs759927335", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759927335" }, { "id": "rs759927335", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759927335" }, { "id": "rs759927335", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759927335#frequency_tab" }, { "id": "rs759927335", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759927335" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NDT->KDT).", "chr_id": "4", "chr_pos": "109746259", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N464", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P05156-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05156-1.466.466", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P05156-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P05156-1.480.480", "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": 30 }, { "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": 29 }, { "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": 29 } ], "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": 29 }, { "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": 29 }, { "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": 29 } ], "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P05156-1.494.494", "start_pos": 494, "end_pos": 494, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "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": "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": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29671580", "url": "https://glygen.org/publication/PubMed/29671580" } ] }, { "title": "Glycoproteomic analysis of the secretome of human endothelial cells.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Yin X, Bern M, Xing Q, Ho J, Viner R, Mayr M", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "23345538", "url": "https://glygen.org/publication/PubMed/23345538" } ] }, { "title": "Structural basis for complement factor I control and its disease-associated sequence polymorphisms.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Roversi P, Johnson S, Caesar JJ, McLean F, Leath KJ, Tsiftsoglou SA, Morgan BP, Harris CL, Sim RB, Lea SM", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352" } ] } ], "crossref": [ { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "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": "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": "23345538", "url": "https://glygen.org/publication/PubMed/23345538", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2XRC", "url": "https://www.rcsb.org/structure/2XRC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "5O32", "url": "https://www.rcsb.org/structure/5O32", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2XRC|D|476", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|C|476", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|B|476", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|A|476", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|J|494", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|I|494", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs1723931486", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1723931486", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1723931486", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1723931486", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "REKDNERVFSLQWGEVKLIS", "down_seq": "CSKFYGNRFYEKEMECAGTY", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G06247RL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G22310AV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G24528MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G26330YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G27126ED", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G28681TP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISNCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G39188ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G40574BA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "29671580", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29671580" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G49329XU", "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": "Asn494", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G51653BI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G57776ZU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G63041LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G70888PK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G71569SN", "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": "Asn494", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G72747WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G80586MF", "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": "Asn494", "evidence": [ { "id": "23345538", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23345538" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G90575OW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G92406TI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G94390IS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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": "G95865ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LISnCSK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "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=2XRC&bu=0&command=select+.D:476;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn494", "evidence": [ { "id": "P05156", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "id": "21768352", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21768352" }, { "id": "2XRC", "database": "PDB", "url": "https://www.rcsb.org/sequence/2XRC" }, { "id": "5O32", "database": "PDB", "url": "https://www.rcsb.org/structure/5O32" } ] } ], "snv": [ { "evidence": [ { "id": "rs1723931486", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1723931486" }, { "id": "rs1723931486", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1723931486" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCS->TCS).", "chr_id": "4", "chr_pos": "109742544", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N494", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P05156-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P05156-1.480.480", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05156-1.496.496", "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": 45 }, { "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": 44 }, { "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": 44 } ], "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": 44 }, { "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": 44 }, { "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": 44 } ], "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P05156-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "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": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Structural basis for complement factor I control and its disease-associated sequence polymorphisms.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Roversi P, Johnson S, Caesar JJ, McLean F, Leath KJ, Tsiftsoglou SA, Morgan BP, Harris CL, Sim RB, Lea SM", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352" } ] } ], "crossref": [ { "id": "P05156@N536", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N536", "database": "GPTwiki", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2XRC", "url": "https://www.rcsb.org/structure/2XRC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "5O32", "url": "https://www.rcsb.org/structure/5O32", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2XRC|D|518", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|C|518", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|B|518", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|A|518", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|J|536", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|I|536", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "rs1314998523", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314998523", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1314998523", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1314998523#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1314998523", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314998523", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1336453366", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1336453366", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1336453366", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1336453366#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1336453366", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1336453366", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1357609555", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357609555", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1357609555", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1357609555#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1357609555", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357609555", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "GSIDACKGDSGGPLVCMDAN", "down_seq": "VTYVWGVVSWGENCGKPEFP", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn536", "evidence": [ { "id": "P05156@N536", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N536" } ] }, { "glytoucan_ac": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn536", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G47737VJ", "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": "Asn536", "evidence": [ { "id": "P05156@N536", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N536" } ] }, { "glytoucan_ac": "G48414YA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn536", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "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=2XRC&bu=0&command=select+.D:518;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn536", "evidence": [ { "id": "P05156", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "21768352", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21768352" }, { "id": "2XRC", "database": "PDB", "url": "https://www.rcsb.org/sequence/2XRC" }, { "id": "5O32", "database": "PDB", "url": "https://www.rcsb.org/structure/5O32" } ] } ], "snv": [ { "evidence": [ { "id": "rs1314998523", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1314998523" }, { "id": "rs1314998523", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1314998523#frequency_tab" }, { "id": "rs1314998523", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1314998523" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->DVT).", "chr_id": "4", "chr_pos": "109741039", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N536", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1336453366", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1336453366" }, { "id": "rs1336453366", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1336453366#frequency_tab" }, { "id": "rs1336453366", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1336453366" } ], "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": "4", "chr_pos": "109741037", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N536", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1357609555", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357609555" }, { "id": "rs1357609555", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1357609555#frequency_tab" }, { "id": "rs1357609555", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357609555" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NVT->SVT).", "chr_id": "4", "chr_pos": "109741038", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N536", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P05156-1.519.519", "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": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 4 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl", "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": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05156-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Large-scale intact glycopeptide identification by Mascot database search.", "journal": "Scientific reports", "date": "2018", "authors": "Bollineni RC, Koehler CJ, Gislefoss RE, Anonsen JH, Thiede B", "evidence": [ { "database": "GlyConnect", "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ], "reference": [ { "type": "PubMed", "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424" } ] }, { "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": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Structural basis for complement factor I control and its disease-associated sequence polymorphisms.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Roversi P, Johnson S, Caesar JJ, McLean F, Leath KJ, Tsiftsoglou SA, Morgan BP, Harris CL, Sim RB, Lea SM", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "reference": [ { "type": "PubMed", "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352" } ] }, { "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": "P05156@N70", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N70", "database": "GPTwiki", "categories": [ "Other" ] }, { "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "742", "url": "https://glyconnect.expasy.org/browser/proteins/742", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "29391424", "url": "https://glygen.org/publication/PubMed/29391424", "database": "PubMed", "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": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21768352", "url": "https://glygen.org/publication/PubMed/21768352", "database": "PubMed", "categories": [ "Other" ] }, { "id": "2XRC", "url": "https://www.rcsb.org/structure/2XRC", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "5O32", "url": "https://www.rcsb.org/structure/5O32", "database": "PDB", "categories": [ "3D Structure" ] }, { "id": "2XRC|D|52", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|C|52", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|B|52", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "2XRC|A|52", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|H|70", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "5O32|D|70", "url": "", "database": "", "categories": [ "Other" ] }, { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs749553820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749553820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749553820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749553820", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749553820", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749553820#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749553820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749553820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "PWQRCIEGTCVCKLPYQCPK", "down_seq": "GTAVCATNRRSFPTYCQQKS", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "P05156@N70", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P05156@N70" }, { "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": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G22310AV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "G32788FZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G56784JY", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "29391424", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29391424" }, { "id": "742", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/742" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "G73430PD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "NGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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": "nGTAVCATNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "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=2XRC&bu=0&command=select+.D:52;+center+selection;+zoom+selection" }, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn70", "evidence": [ { "id": "P05156", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P05156#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "21768352", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21768352" }, { "id": "2XRC", "database": "PDB", "url": "https://www.rcsb.org/sequence/2XRC" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "5O32", "database": "PDB", "url": "https://www.rcsb.org/structure/5O32" } ] } ], "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NGT->IGT).", "chr_id": "4", "chr_pos": "109766673", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "N70", "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": "rs749553820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749553820" }, { "id": "rs749553820", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749553820" }, { "id": "rs749553820", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749553820#frequency_tab" }, { "id": "rs749553820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749553820" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->TGT).", "chr_id": "4", "chr_pos": "109766673", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N70", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P05156-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P05156-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P05156-1.81.81", "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": 18 }, { "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": 17 }, { "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": 17 } ], "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": 17 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 17 }, { "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": 17 } ], "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05156-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "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": "P05156", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05156" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "P05156", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05156" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P05156", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05156", "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": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "P05156", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05156" }, { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "P05156-1.19.19", "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": "P05156-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1316844995", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316844995", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1316844995", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1316844995#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1316844995", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316844995", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YCQQKSLECLHPGTKFLNNG", "down_seq": "CTAEGKFSVSLKHGNTDSEG", "snv": [ { "evidence": [ { "id": "rs1316844995", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1316844995" }, { "id": "rs1316844995", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1316844995#frequency_tab" }, { "id": "rs1316844995", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1316844995" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NGT->NGR).", "chr_id": "4", "chr_pos": "109766568", "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": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P05156-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05156-1.111.111", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05156-1.113.113", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.111.111", "start_pos": 111, "end_pos": 111, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs189153845", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs189153845", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs189153845", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs189153845", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs189153845", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs189153845", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs189153845", "url": "http://gnomad.broadinstitute.org/awesome?query=rs189153845", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs189153845", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs189153845", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LECLHPGTKFLNNGTCTAEG", "down_seq": "FSVSLKHGNTDSEGIVEVKL", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" }, { "id": "rs189153845", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs189153845" }, { "id": "rs189153845", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs189153845" }, { "id": "rs189153845", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs189153845" }, { "id": "rs189153845", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs189153845" }, { "id": "rs189153845", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs189153845" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KFS->NFS).", "chr_id": "4", "chr_pos": "109764686", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K111", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P05156-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P05156-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P05156-1.113.113", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs150610189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150610189", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150610189", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150610189", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs150610189", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150610189#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs150610189", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150610189", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs150610189", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150610189", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CLHPGTKFLNNGTCTAEGKF", "down_seq": "VSLKHGNTDSEGIVEVKLVD", "snv": [ { "evidence": [ { "id": "rs150610189", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150610189" }, { "id": "rs150610189", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150610189" }, { "id": "rs150610189", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs150610189#frequency_tab" }, { "id": "rs150610189", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs150610189" }, { "id": "rs150610189", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150610189" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SVS->NVS).", "chr_id": "4", "chr_pos": "109764681", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S113", "disease": [ { "disease_id": "DOID:0110025", "recommended_name": { "id": "DOID:0110025", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110025", "name": "age related macular degeneration 13", "description": "An age related macular degeneration conferred by heterozygous mutation in the CFI gene on chromosome 4q25." }, "synonyms": [ { "id": "DOID:0110025", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0110025", "name": "ARMD13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "age related macular degeneration 13", "description": "An inherited susceptibility or predisposition to developing age related macular degeneration in which the cause of the disease is a mutation in the CFI gene." }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "ARMD13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "CFI age-related macular degeneration", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "age related macular degeneration type 13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "age-related macular degeneration caused by mutation in CFI", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "macular degeneration, age-related, 13, susceptibility to", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "macular degeneration, age-related, type 13", "description": "" }, { "id": "MONDO:0014189", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0014189", "name": "macular degeneration, age-related, 13", "description": "" }, { "id": "MIM:615439", "resource": "MIM", "url": "https://www.omim.org/entry/615439", "name": "Macular degeneration, age-related, 13", "description": "Macular degeneration, age-related, 13" } ], "unlinked_id_list": [], "evidence": [ { "id": "615439", "database": "MIM", "url": "https://www.omim.org/entry/615439" }, { "id": "0110025", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0110025" } ] }, { "disease_id": "DOID:0050419", "recommended_name": { "id": "DOID:0050419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050419", "name": "complement factor I deficiency", "description": "A complement deficiency that is characterized by recurrent pyogenic bacterial infections that is the result of complement component 3 deficiency." }, "synonyms": [ { "id": "DOID:0050419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050419", "name": "C3 INACTIVATOR DEFICIENCY", "description": "" }, { "id": "DOID:0050419", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0050419", "name": "COMPLEMENT COMPONENT 3 INACTIVATOR DEFICIENCY", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "complement factor I deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "C3 inactivator deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "complement component 3 inactivator deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "complement factor I deficiency", "description": "" }, { "id": "MONDO:0012594", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012594", "name": "CFID", "description": "" }, { "id": "MIM:610984", "resource": "MIM", "url": "https://www.omim.org/entry/610984", "name": "Complement factor I deficiency", "description": "Complement factor I deficiency" } ], "unlinked_id_list": [], "evidence": [ { "id": "610984", "database": "MIM", "url": "https://www.omim.org/entry/610984" }, { "id": "0050419", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0050419" } ] } ], "keywords": [ "ebi", "somatic", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P05156-1.103.103", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P05156-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05156-1.111.111", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "P05156-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1357120518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357120518", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1357120518", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357120518", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EGIVEVKLVDQDKTMFICKS", "down_seq": "WSMREANVACLDLGFQQGAD", "snv": [ { "evidence": [ { "id": "rs1357120518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1357120518" }, { "id": "rs1357120518", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1357120518" } ], "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 (SWS->NWS).", "chr_id": "4", "chr_pos": "109764588", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S144", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "P05156-1.153.153", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2545449970", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2545449970", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DQDKTMFICKSSWSMREANV", "down_seq": "CLDLGFQQGADTQRRFKLSD", "snv": [ { "evidence": [ { "id": "rs2545449970", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2545449970" } ], "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": "4", "chr_pos": "109764562", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A153", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P05156-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P05156-1.173.173", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778279488", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778279488", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778279488", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778279488", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778279488", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778279488", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ACLDLGFQQGADTQRRFKLS", "down_seq": "LSINSTECLHVHCRGLETSL", "snv": [ { "evidence": [ { "id": "rs778279488", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778279488" }, { "id": "rs778279488", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778279488" }, { "id": "rs778279488", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778279488" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "4", "chr_pos": "109761658", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D173", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05156-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P05156-1.177.177", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P05156-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P05156-1.179.179", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs71603044", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs71603044", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs71603044", "url": "https://www.ensembl.org/id/rs71603044", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GFQQGADTQRRFKLSDLSIN", "down_seq": "TECLHVHCRGLETSLAECTF", "snv": [ { "evidence": [ { "id": "rs71603044", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs71603044" }, { "id": "rs71603044", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs71603044" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NST->NPT).", "chr_id": "4", "chr_pos": "109761643", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S178", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "P05156-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05156-1.177.177", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05156-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P05156-1.197.197", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1727075785", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1727075785", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1727075785", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1727075785#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1727075785", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1727075785", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FQQGADTQRRFKLSDLSINS", "down_seq": "ECLHVHCRGLETSLAECTFT", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" }, { "id": "rs1727075785", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1727075785" }, { "id": "rs1727075785", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1727075785#frequency_tab" }, { "id": "rs1727075785", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1727075785" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NST->NSA).", "chr_id": "4", "chr_pos": "109761640", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T179", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P05156-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05156-1.177.177", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05156-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P05156-1.197.197", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.197.197", "start_pos": 197, "end_pos": 197, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSTECLHVHCRGLETSLAEC", "down_seq": "FTKRRTMGYQDFADVVCYTQ", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TFT->NFT).", "chr_id": "4", "chr_pos": "109761585", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T197", "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": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P05156-1.177.177", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P05156-1.178.178", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P05156-1.179.179", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1309017956", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309017956", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309017956", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309017956#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1309017956", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309017956", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MKLLHVFLLFLCFHLRFC", "down_seq": "VTYTSQEDLVEKKCLAKKYT", "snv": [ { "evidence": [ { "id": "rs1309017956", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309017956" }, { "id": "rs1309017956", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1309017956#frequency_tab" }, { "id": "rs1309017956", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309017956" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVT->NVT).", "chr_id": "4", "chr_pos": "109801915", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K19", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P05156-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P05156-1.37.37", "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": "P05156-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SQYQCNGEVDCITGEDEVGC", "down_seq": "GFASVTQEETEILTADMDAE", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "109760272", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A294", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "P05156-1.306.306", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.306.306", "start_pos": 306, "end_pos": 306, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "TGEDEVGCAGFASVTQEETE", "down_seq": "LTADMDAERRRIKSLLPKLS", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "I", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (ILT->NLT).", "chr_id": "4", "chr_pos": "109752491", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "I306", "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": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P05156-1.294.294", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1179323501", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1179323501", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1179323501", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1179323501", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "AERRRIKSLLPKLSCGVKNR", "down_seq": "HIRRKRIVGGKRAQLGDLPW", "snv": [ { "evidence": [ { "id": "rs1179323501", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1179323501" }, { "id": "rs1179323501", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1179323501" } ], "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": "4", "chr_pos": "109749545", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M333", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "P05156-1.336.336", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RRIKSLLPKLSCGVKNRMHI", "down_seq": "RKRIVGGKRAQLGDLPWQVA", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "4", "chr_pos": "109749537", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R336", "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" ] }, { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "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 (3).", "chr_id": "4", "chr_pos": "109749536", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R336", "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": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P05156-1.333.333", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P05156-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1280667820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1280667820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1280667820", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1280667820#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1280667820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1280667820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "FCKVTYTSQEDLVEKKCLAK", "down_seq": "YTHLSCDKVFCQPWQRCIEG", "snv": [ { "evidence": [ { "id": "rs1280667820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1280667820" }, { "id": "rs1280667820", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1280667820#frequency_tab" }, { "id": "rs1280667820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1280667820" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KYT->NYT).", "chr_id": "4", "chr_pos": "109766771", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K37", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P05156-1.19.19", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.385.385", "start_pos": 385, "end_pos": 385, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1356737725", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1356737725", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1356737725", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1356737725", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CGGIYIGGCWILTAAHCLRA", "down_seq": "KTHRYQIWTTVVDWIHPDLK", "snv": [ { "evidence": [ { "id": "rs1356737725", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1356737725" }, { "id": "rs1356737725", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1356737725" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKT->NKT).", "chr_id": "4", "chr_pos": "109746497", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S385", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.424.424", "start_pos": 424, "end_pos": 424, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748063552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748063552", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748063552", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748063552", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs748063552", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748063552", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748063552", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748063552", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs748063552", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748063552", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LKRIVIEYVDRIIFHENYNA", "down_seq": "TYQNDIALIEMKKDGNKKDC", "snv": [ { "evidence": [ { "id": "rs748063552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748063552" }, { "id": "rs748063552", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748063552" }, { "id": "rs748063552", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748063552" }, { "id": "rs748063552", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748063552" }, { "id": "rs748063552", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748063552" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAG->NAC).", "chr_id": "4", "chr_pos": "109746381", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G424", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs748063552", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748063552" }, { "id": "rs748063552", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs748063552" }, { "id": "rs748063552", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748063552" }, { "id": "rs748063552", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748063552" } ], "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": "4", "chr_pos": "109746381", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G424", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "P05156-1.430.430", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P05156-1.431.431", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P05156-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs754872751", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754872751", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754872751", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754872751", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754872751", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754872751", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EYVDRIIFHENYNAGTYQND", "down_seq": "ALIEMKKDGNKKDCELPRSI", "snv": [ { "evidence": [ { "id": "rs754872751", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754872751" }, { "id": "rs754872751", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754872751" }, { "id": "rs754872751", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754872751" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDI->NDT).", "chr_id": "4", "chr_pos": "109746362", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I430", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P05156-1.424.424", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05156-1.431.431", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YVDRIIFHENYNAGTYQNDI", "down_seq": "LIEMKKDGNKKDCELPRSIP", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "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 (4).", "chr_id": "4", "chr_pos": "109746360", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A431", "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:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID: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": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P05156-1.424.424", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05156-1.430.430", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.465.465", "start_pos": 465, "end_pos": 465, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ELPRSIPACVPWSPYLFQPN", "down_seq": "TCIVSGWGREKDNERVFSLQ", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DTC->NTC).", "chr_id": "4", "chr_pos": "109746258", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D465", "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": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P05156-1.464.464", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05156-1.466.466", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P05156-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P05156-1.480.480", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.466.466", "start_pos": 466, "end_pos": 466, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2545375506", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2545375506", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LPRSIPACVPWSPYLFQPND", "down_seq": "CIVSGWGREKDNERVFSLQW", "snv": [ { "evidence": [ { "id": "rs2545375506", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2545375506" } ], "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 (NDT->NDR).", "chr_id": "4", "chr_pos": "109746254", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T466", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P05156-1.464.464", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05156-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P05156-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P05156-1.480.480", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.479.479", "start_pos": 479, "end_pos": 479, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YLFQPNDTCIVSGWGREKDN", "down_seq": "RVFSLQWGEVKLISNCSKFY", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "4", "chr_pos": "109742590", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E479", "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: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": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P05156-1.464.464", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P05156-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P05156-1.466.466", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05156-1.480.480", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P05156-1.494.494", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P05156-1.496.496", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.480.480", "start_pos": 480, "end_pos": 480, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs41304872", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs41304872", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs41304872", "url": "https://www.ensembl.org/id/rs41304872", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LFQPNDTCIVSGWGREKDNE", "down_seq": "VFSLQWGEVKLISNCSKFYG", "snv": [ { "evidence": [ { "id": "rs41304872", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs41304872" }, { "id": "rs41304872", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs41304872" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NER->NES).", "chr_id": "4", "chr_pos": "109742585", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R480", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P05156-1.464.464", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P05156-1.465.465", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P05156-1.466.466", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05156-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P05156-1.494.494", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P05156-1.496.496", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P05156-1.496.496", "start_pos": 496, "end_pos": 496, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750850949", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750850949", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758942583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758942583", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758942583", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758942583", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758942583", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758942583#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs758942583", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758942583", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KDNERVFSLQWGEVKLISNC", "down_seq": "KFYGNRFYEKEMECAGTYDG", "snv": [ { "evidence": [ { "id": "rs750850949", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750850949" } ], "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 (NCS->NCF).", "chr_id": "4", "chr_pos": "109742538", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S496", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs758942583", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758942583" }, { "id": "rs758942583", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758942583" }, { "id": "rs758942583", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs758942583#frequency_tab" }, { "id": "rs758942583", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758942583" } ], "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 (NCS->NCP).", "chr_id": "4", "chr_pos": "109742539", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S496", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P05156-1.479.479", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P05156-1.480.480", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P05156-1.494.494", "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": "P05156-1.519.519", "start_pos": 519, "end_pos": 519, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Genetics of HUS: the impact of MCP, CFH, and IF mutations on clinical presentation, response to treatment, and outcome.", "journal": "Blood", "date": "2006", "authors": "Caprioli J, Noris M, Brioschi S, Pianetti G, Castelletti F, Bettinaglio P, Mele C, Bresin E, Cassis L, Gamba S, Porrati F, Bucchioni S, Monteferrante G, Fang CJ, Liszewski MK, Kavanagh D, Atkinson JP, Remuzzi G", "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" }, { "database": "dbSNP", "id": "rs121964918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs121964918" } ], "reference": [ { "type": "PubMed", "id": "16621965", "url": "https://glygen.org/publication/PubMed/16621965" } ] } ], "crossref": [ { "id": "P05156", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs121964918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs121964918", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs121964918", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs121964918", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs121964918", "url": "https://www.ncbi.nlm.nih.gov/snp/rs121964918#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs121964918", "url": "http://gnomad.broadinstitute.org/awesome?query=rs121964918", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "16621965", "url": "https://glygen.org/publication/PubMed/16621965", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs121964918", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs121964918", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YGNRFYEKEMECAGTYDGSI", "down_seq": "ACKGDSGGPLVCMDANNVTY", "snv": [ { "evidence": [ { "id": "P05156", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P05156" }, { "id": "rs121964918", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs121964918" }, { "id": "rs121964918", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs121964918" }, { "id": "rs121964918", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs121964918#frequency_tab" }, { "id": "rs121964918", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs121964918" }, { "id": "16621965", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16621965" }, { "id": "rs121964918", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs121964918" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DAC->NAC).", "chr_id": "4", "chr_pos": "109741090", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D519", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P05156-1.536.536", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P05156-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2126224479", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2126224479", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2126224479", "url": "https://www.ensembl.org/id/rs2126224479", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QRCIEGTCVCKLPYQCPKNG", "down_seq": "AVCATNRRSFPTYCQQKSLE", "snv": [ { "evidence": [ { "id": "rs2126224479", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2126224479" }, { "id": "rs2126224479", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2126224479" } ], "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 (NGT->NGA).", "chr_id": "4", "chr_pos": "109766668", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T72", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P05156-1.70.70", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P05156-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P05156-1.81.81", "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": "P05156-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1727792524", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1727792524", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1727792524", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1727792524#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VCKLPYQCPKNGTAVCATNR", "down_seq": "SFPTYCQQKSLECLHPGTKF", "snv": [ { "evidence": [ { "id": "rs1727792524", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1727792524" }, { "id": "rs1727792524", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1727792524#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRS).", "chr_id": "4", "chr_pos": "109766642", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R80", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P05156-1.70.70", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P05156-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P05156-1.81.81", "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": "P05156-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P05156-1", "length": 583, "uniprot_id": "CFAI_HUMAN", "protein_name": "Complement factor I", "refseq_ac": "NP_001317964", "refseq_name": "complement factor I isoform 3 preproprotein", "gene_name": "CFI", "gene_names_uniprotkb": "CFI; IF", "gene_names_refseq": "AHUS3; ARMD13; C3BINA; C3b-INA; CFI; FI; IF; KAF", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P05156", "url": "https://www.uniprot.org/uniprotkb/P05156" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P05156", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05156" } ], "reference": [ { "type": "PubMed", "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261" } ] } ], "crossref": [ { "id": "P05156", "url": "https://www.iedb.org/epitope/P05156", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P05156", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05156", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CKLPYQCPKNGTAVCATNRR", "down_seq": "FPTYCQQKSLECLHPGTKFL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "P05156", "url": "https://www.iedb.org/epitope/P05156" }, { "database": "iPTMnet", "id": "P05156", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P05156" }, { "database": "PubMed", "id": "31848261", "url": "https://glygen.org/publication/PubMed/31848261" } ], "site_lbl": "Ser81" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "103", "end_pos": "103" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" } ] }, { "type": "snv", "site_list": [ { "start_pos": "105", "end_pos": "105" }, { "start_pos": "111", "end_pos": "111" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "197", "end_pos": "197" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "294", "end_pos": "294" }, { "start_pos": "306", "end_pos": "306" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "424", "end_pos": "424" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "464", "end_pos": "464" }, { "start_pos": "465", "end_pos": "465" }, { "start_pos": "466", "end_pos": "466" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "494", "end_pos": "494" }, { "start_pos": "496", "end_pos": "496" }, { "start_pos": "519", "end_pos": "519" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "80", "end_pos": "80" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "81", "end_pos": "81" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P05156-1.70.70", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P05156-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P05156-1.80.80", "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": "Q05397-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "rs1466770413", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1466770413", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1466770413", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1466770413#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1466770413", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1466770413", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1600927451", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600927451", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1600927451", "url": "https://www.ensembl.org/id/rs1600927451", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MAAAYLDPNLNHTP", "down_seq": "SSTKTHLGTGMERSPGAMER", "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": "AAAYLDPNLNHTPNSSTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn15", "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": "rs1466770413", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1466770413" }, { "id": "rs1466770413", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1466770413#frequency_tab" }, { "id": "rs1466770413", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1466770413" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->DSS).", "chr_id": "8", "chr_pos": "140890695", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N15", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1600927451", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1600927451" }, { "id": "rs1600927451", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1600927451" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->KSS).", "chr_id": "8", "chr_pos": "140890693", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N15", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q05397-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05397-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q05397-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q05397-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q05397-1.29.29", "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": "Q05397-1.458.458", "start_pos": 458, "end_pos": 458, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "rs2100063188", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100063188", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2100063188", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2100063188#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2100063188", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2100063188", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs753752073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753752073", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753752073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753752073", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753752073", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753752073#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753752073", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753752073", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QGIYMSPENPALAVAIKTCK", "down_seq": "CTSDSVREKFLQEALTMRQF", "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": "NCTSDSVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn458", "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": "rs2100063188", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100063188" }, { "id": "rs2100063188", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2100063188#frequency_tab" }, { "id": "rs2100063188", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2100063188" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCT->HCT).", "chr_id": "8", "chr_pos": "140752277", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N458", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs753752073", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753752073" }, { "id": "rs753752073", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753752073" }, { "id": "rs753752073", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753752073#frequency_tab" }, { "id": "rs753752073", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753752073" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NCT->KCT).", "chr_id": "8", "chr_pos": "140752275", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N458", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q05397-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q05397-1.460.460", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.474.474", "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": "Q05397-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAcylation regulates integrin-mediated cell adhesion and migration via formation of focal adhesion complexes.", "journal": "The Journal of biological chemistry", "date": "2019", "authors": "Xu Z, Isaji T, Fukuda T, Wang Y, Gu J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" } ], "reference": [ { "type": "PubMed", "id": "30587575", "url": "https://glygen.org/publication/PubMed/30587575" } ] }, { "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": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" } ], "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": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "O-GlcNAc Transferase Recognizes Protein Substrates Using an Asparagine Ladder in the Tetratricopeptide Repeat (TPR) Superhelix.", "journal": "Journal of the American Chemical Society", "date": "2018", "authors": "Levine ZG, Fan C, Melicher MS, Orman M, Benjamin T, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" } ], "reference": [ { "type": "PubMed", "id": "29485866", "url": "https://glygen.org/publication/PubMed/29485866" } ] }, { "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": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] } ], "crossref": [ { "id": "30587575", "url": "https://glygen.org/publication/PubMed/30587575", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29485866", "url": "https://glygen.org/publication/PubMed/29485866", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "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": "30587575", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30587575" }, { "id": "Q05397", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q05397" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "29485866", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29485866" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q05397-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q05397-1.17.17", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.1034.1034", "start_pos": 1034, "end_pos": 1034, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Interaction of Hic-5, A senescence-related protein, with focal adhesion kinase.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Fujita H, Kamiguchi K, Cho D, Shibanuma M, Morimoto C, Tachibana K", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9756887", "url": "https://glygen.org/publication/PubMed/9756887" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9756887", "url": "https://glygen.org/publication/PubMed/9756887", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QEYKKQMLTAAHALAVDAKN", "down_seq": "LDVIDQARLKMLGQTRPH", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "S", "comment": "Loss of interaction with TGFB1I1.", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "9756887", "url": "https://glygen.org/publication/PubMed/9756887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q05397-1.1016.1016", "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": "Q05397-1.397.397", "start_pos": 397, "end_pos": 397, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulation of the PH-domain-containing tyrosine kinase Etk by focal adhesion kinase through the FERM domain.", "journal": "Nature cell biology", "date": "2001", "authors": "Chen R, Kim O, Li M, Xiong X, Guan JL, Kung HJ, Chen H, Shimizu Y, Qiu Y", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11331870", "url": "https://glygen.org/publication/PubMed/11331870" } ] }, { "title": "Tyrosine phosphorylation of Crk-associated substrates by focal adhesion kinase. A putative mechanism for the integrin-mediated tyrosine phosphorylation of Crk-associated substrates.", "journal": "The Journal of biological chemistry", "date": "1997", "authors": "Tachibana K, Urano T, Fujita H, Ohashi Y, Kamiguchi K, Iwata S, Hirai H, Morimoto C", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9360983", "url": "https://glygen.org/publication/PubMed/9360983" } ] }, { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] }, { "title": "Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein.", "journal": "The Biochemical journal", "date": "2003", "authors": "Relou IA, Bax LA, van Rijn HJ, Akkerman JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ] }, { "title": "Identification of Src-specific phosphorylation site on focal adhesion kinase: dissection of the role of Src SH2 and catalytic functions and their consequences for tumor cell behavior.", "journal": "Cancer research", "date": "2005", "authors": "Brunton VG, Avizienyte E, Fincham VJ, Serrels B, Metcalf CA 3rd, Sawyer TK, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ] }, { "title": "Activation of the focal adhesion kinase signaling pathway by structural alterations in the carboxyl-terminal region of c-Crk II.", "journal": "Oncogene", "date": "2001", "authors": "Zvara A, Fajardo JE, Escalante M, Cotton G, Muir T, Kirsch KH, Birge RB", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11314030", "url": "https://glygen.org/publication/PubMed/11314030" } ] }, { "title": "Tyr-863 phosphorylation enhances focal adhesion kinase autophosphorylation at Tyr-397.", "journal": "Oncogene", "date": "2002", "authors": "Leu TH, Maa MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "12370821", "url": "https://glygen.org/publication/PubMed/12370821" } ] }, { "title": "Effects of HER2 overexpression on cell signaling networks governing proliferation and migration.", "journal": "Molecular systems biology", "date": "2006", "authors": "Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Autophosphorylation of the focal adhesion kinase, pp125FAK, directs SH2-dependent binding of pp60src.", "journal": "Molecular and cellular biology", "date": "1994", "authors": "Schaller MD, Hildebrand JD, Shannon JD, Fox JW, Vines RR, Parsons JT", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "7509446", "url": "https://glygen.org/publication/PubMed/7509446" } ] }, { "title": "Tyrosine phosphorylation of focal adhesion kinase at sites in the catalytic domain regulates kinase activity: a role for Src family kinases.", "journal": "Molecular and cellular biology", "date": "1995", "authors": "Calalb MB, Polte TR, Hanks SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ] }, { "title": "LRRK2 Inhibits FAK Activity by Promoting FERM-mediated Autoinhibition of FAK and Recruiting the Tyrosine Phosphatase, SHP-2.", "journal": "Experimental neurobiology", "date": "2016", "authors": "Choi I, Byun JW, Park SM, Jou I, Joe EH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27790061", "url": "https://glygen.org/publication/PubMed/27790061" } ] }, { "title": "v-Src induces tyrosine phosphorylation of focal adhesion kinase independently of tyrosine 397 and formation of a complex with Src.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "McLean GW, Fincham VJ, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10816598", "url": "https://glygen.org/publication/PubMed/10816598" } ] }, { "title": "Distinct FAK-Src activation events promote alpha5beta1 and alpha4beta1 integrin-stimulated neuroblastoma cell motility.", "journal": "Oncogene", "date": "2008", "authors": "Wu L, Bernard-Trifilo JA, Lim Y, Lim ST, Mitra SK, Uryu S, Chen M, Pallen CJ, Cheung NK, Mikolon D, Mielgo A, Stupack DG, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17828307", "url": "https://glygen.org/publication/PubMed/17828307" } ] }, { "title": "Activation of focal adhesion kinase through an interaction with \u03b24 integrin contributes to tumorigenicity of colon cancer.", "journal": "FEBS letters", "date": "2016-06", "authors": "Tai Yu-Ling, Lai I-Rue, Peng Yu-Ju, Ding Shih-Torng, Shen Tang-Long", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27178753", "url": "https://glygen.org/publication/PubMed/27178753" } ] }, { "title": "Involvement of focal adhesion kinase in inhibition of motility of human breast cancer cells by sphingosine 1-phosphate.", "journal": "Experimental cell research", "date": "1999", "authors": "Wang F, Nohara K, Olivera A, Thompson EW, Spiegel S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10047444", "url": "https://glygen.org/publication/PubMed/10047444" } ] }, { "title": "Requirement of phosphatidylinositol 3-kinase in focal adhesion kinase-promoted cell migration.", "journal": "The Journal of biological chemistry", "date": "1999-04-30", "authors": "Reiske H R, Kao S C, Cary L A, Guan J L, Lai J F, Chen H C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10212207", "url": "https://glygen.org/publication/PubMed/10212207" } ] }, { "title": "PTEN interactions with focal adhesion kinase and suppression of the extracellular matrix-dependent phosphatidylinositol 3-kinase/Akt cell survival pathway.", "journal": "The Journal of biological chemistry", "date": "1999-07-16", "authors": "Tamura M, Gu J, Danen E H, Takino T, Miyamoto S, Yamada K M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10400703", "url": "https://glygen.org/publication/PubMed/10400703" } ] }, { "title": "Phosphospecific antibodies reveal focal adhesion kinase activation loop phosphorylation in nascent and mature focal adhesions and requirement for the autophosphorylation site.", "journal": "Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research", "date": "2000-01", "authors": "Ruest P J, Roy S, Shi E, Mernaugh R L, Hanks S K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902" } ] }, { "title": "Integrin-mediated survival signals regulate the apoptotic function of Bax through its conformation and subcellular localization.", "journal": "The Journal of cell biology", "date": "2000", "authors": "Gilmore AP, Metcalfe AD, Romer LH, Streuli CH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10769034", "url": "https://glygen.org/publication/PubMed/10769034" } ] }, { "title": "Type 1 pilus-mediated bacterial invasion of bladder epithelial cells.", "journal": "The EMBO journal", "date": "2000", "authors": "Martinez JJ, Mulvey MA, Schilling JD, Pinkner JS, Hultgren SJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10856226", "url": "https://glygen.org/publication/PubMed/10856226" } ] }, { "title": "Integrin activation and focal complex formation in cardiac hypertrophy.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Laser M, Willey CD, Jiang W, Cooper G 4th, Menick DR, Zile MR, Kuppuswamy D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10958798", "url": "https://glygen.org/publication/PubMed/10958798" } ] }, { "title": "Focal adhesion kinase facilitates platelet-derived growth factor-BB-stimulated ERK2 activation required for chemotaxis migration of vascular smooth muscle cells.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Hauck CR, Hsia DA, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10998418", "url": "https://glygen.org/publication/PubMed/10998418" } ] }, { "title": "Nuclear localization and apoptotic regulation of an amino-terminal domain focal adhesion kinase fragment in endothelial cells.", "journal": "Biochemical and biophysical research communications", "date": "2000", "authors": "Lobo M, Zachary I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591" } ] }, { "title": "Analysis of FAK-associated signaling pathways in the regulation of cell cycle progression.", "journal": "FEBS letters", "date": "2000-12-15", "authors": "Reiske H R, Zhao J, Han D C, Cooper L A, Guan J L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11119718", "url": "https://glygen.org/publication/PubMed/11119718" } ] }, { "title": "Targeting Pyk2 to beta 1-integrin-containing focal contacts rescues fibronectin-stimulated signaling and haptotactic motility defects of focal adhesion kinase-null cells.", "journal": "The Journal of cell biology", "date": "2001", "authors": "Klingbeil CK, Hauck CR, Hsia DA, Jones KC, Reider SR, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924" } ] }, { "title": "The v-Src SH3 domain facilitates a cell adhesion-independent association with focal adhesion kinase.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Hauck CR, Hunter T, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11278488", "url": "https://glygen.org/publication/PubMed/11278488" } ] }, { "title": "Alterations in the focal adhesion kinase/Src signal transduction pathway correlate with increased migratory capacity of prostate carcinoma cells.", "journal": "Oncogene", "date": "2001", "authors": "Slack JK, Adams RB, Rovin JD, Bissonette EA, Stoker CE, Parsons JT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11313859", "url": "https://glygen.org/publication/PubMed/11313859" } ] }, { "title": "Plasma membrane-associated pY397FAK is a marker of cytotrophoblast invasion in vivo and in vitro.", "journal": "The American journal of pathology", "date": "2001", "authors": "Ilic D, Genbacev O, Jin F, Caceres E, Almeida EA, Bellingard-Dubouchaud V, Schaefer EM, Damsky CH, Fisher SJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11438458", "url": "https://glygen.org/publication/PubMed/11438458" } ] }, { "title": "The LD4 motif of paxillin regulates cell spreading and motility through an interaction with paxillin kinase linker (PKL).", "journal": "The Journal of cell biology", "date": "2001", "authors": "West KA, Zhang H, Brown MC, Nikolopoulos SN, Riedy MC, Horwitz AF, Turner CE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11448998", "url": "https://glygen.org/publication/PubMed/11448998" } ] }, { "title": "Focal adhesion kinase is involved in mechanosensing during fibroblast migration.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2001-09-25", "authors": "Wang H B, Dembo M, Hanks S K, Wang Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11572981", "url": "https://glygen.org/publication/PubMed/11572981" } ] }, { "title": "Inhibition of focal adhesion kinase expression or activity disrupts epidermal growth factor-stimulated signaling promoting the migration of invasive human carcinoma cells.", "journal": "Cancer research", "date": "2001", "authors": "Hauck CR, Sieg DJ, Hsia DA, Loftus JC, Gaarde WA, Monia BP, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11585739", "url": "https://glygen.org/publication/PubMed/11585739" } ] }, { "title": "Signalling of GPI-anchored CD157 via focal adhesion kinase in MCA102 fibroblasts.", "journal": "FEBS letters", "date": "2001", "authors": "Liang F, Qi RZ, Chang CF", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11602246", "url": "https://glygen.org/publication/PubMed/11602246" } ] }, { "title": "Uniaxial cyclic stretch induces focal adhesion kinase (FAK) tyrosine phosphorylation followed by mitogen-activated protein kinase (MAPK) activation.", "journal": "Biochemical and biophysical research communications", "date": "2001-10-26", "authors": "Wang J G, Miyazu M, Matsushita E, Sokabe M, Naruse K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11606050", "url": "https://glygen.org/publication/PubMed/11606050" } ] }, { "title": "Role of tyrosine phosphorylation in ligand-independent sequestration of CXCR4 in human primary monocytes-macrophages.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Wang J, Guan E, Roderiquez G, Calvert V, Alvarez R, Norcross MA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11668182", "url": "https://glygen.org/publication/PubMed/11668182" } ] }, { "title": "Src mediates stimulation by vascular endothelial growth factor of the phosphorylation of focal adhesion kinase at tyrosine 861, and migration and anti-apoptosis in endothelial cells.", "journal": "The Biochemical journal", "date": "2001", "authors": "Abu-Ghazaleh R, Kabir J, Jia H, Lobo M, Zachary I", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11696015", "url": "https://glygen.org/publication/PubMed/11696015" } ] }, { "title": "FAK regulates tyrosine phosphorylation of CAS, paxillin, and PYK2 in cells expressing v-Src, but is not a critical determinant of v-Src transformation.", "journal": "Journal of cellular biochemistry", "date": "2002", "authors": "Roy Shyamali, Ruest Paul J, Hanks Steven K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11787067", "url": "https://glygen.org/publication/PubMed/11787067" } ] }, { "title": "Differential regulation of components of the focal adhesion complex by heregulin: role of phosphatase SHP-2.", "journal": "Journal of cellular physiology", "date": "2002", "authors": "Vadlamudi RK, Adam L, Nguyen D, Santos M, Kumar R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11807823", "url": "https://glygen.org/publication/PubMed/11807823" } ] }, { "title": "The role of the dynamics of focal adhesion kinase in the mechanotaxis of endothelial cells.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2002", "authors": "Li S, Butler P, Wang Y, Hu Y, Han DC, Usami S, Guan JL, Chien S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11891289", "url": "https://glygen.org/publication/PubMed/11891289" } ] }, { "title": "SRC catalytic but not scaffolding function is needed for integrin-regulated tyrosine phosphorylation, cell migration, and cell spreading.", "journal": "Molecular and cellular biology", "date": "2002", "authors": "Cary LA, Klinghoffer RA, Sachsenmaier C, Cooper JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11909938", "url": "https://glygen.org/publication/PubMed/11909938" } ] }, { "title": "Association of Grb7 with phosphoinositides and its role in the regulation of cell migration.", "journal": "The Journal of biological chemistry", "date": "2002", "authors": "Shen TL, Han DC, Guan JL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12021278", "url": "https://glygen.org/publication/PubMed/12021278" } ] }, { "title": "Staurosporine induces endothelial cell apoptosis via focal adhesion kinase dephosphorylation and focal adhesion disassembly independent of focal adhesion kinase proteolysis.", "journal": "The Biochemical journal", "date": "2002", "authors": "Kabir J, Lobo M, Zachary I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12084011", "url": "https://glygen.org/publication/PubMed/12084011" } ] }, { "title": "Antiapoptotic action of focal adhesion kinase (FAK) against ionizing radiation.", "journal": "Antioxidants & redox signaling", "date": "2002", "authors": "Kasahara T, Koguchi E, Funakoshi M, Aizu-Yokota E, Sonoda Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12215217", "url": "https://glygen.org/publication/PubMed/12215217" } ] }, { "title": "DAP-kinase induces apoptosis by suppressing integrin activity and disrupting matrix survival signals.", "journal": "The Journal of cell biology", "date": "2002", "authors": "Wang WJ, Kuo JC, Yao CC, Chen RH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12370243", "url": "https://glygen.org/publication/PubMed/12370243" } ] }, { "title": "Alternative splicing controls the mechanisms of FAK autophosphorylation.", "journal": "Molecular and cellular biology", "date": "2002", "authors": "Toutant M, Costa A, Studler JM, Kadare G, Carnaud M, Girault JA", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12391143", "url": "https://glygen.org/publication/PubMed/12391143" } ] }, { "title": "Specific interactions of neuronal focal adhesion kinase isoforms with Src kinases and amphiphysin.", "journal": "Journal of neurochemistry", "date": "2003", "authors": "Messina S, Onofri F, Bongiorno-Borbone L, Giovedi S, Valtorta F, Girault JA, Benfenati F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12558988", "url": "https://glygen.org/publication/PubMed/12558988" } ] }, { "title": "Differential regulation of cell motility and invasion by FAK.", "journal": "The Journal of cell biology", "date": "2003-03-03", "authors": "Hsia Datsun A, Mitra Satyajit K, Hauck Christof R, Streblow Daniel N, Nelson Jay A, Ilic Dusko, Huang Shuang, Li Erguang, Nemerow Glen R, Leng Jay, Spencer Kathryn S R, Cheresh David A, Schlaepfer David D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12615911", "url": "https://glygen.org/publication/PubMed/12615911" } ] }, { "title": "Focal adhesion kinase: the first ten years.", "journal": "Journal of cell science", "date": "2003", "authors": "Parsons JT", "evidence": [ { "database": "Reactome", "id": "R-HSA-372708", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-372708" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12640026", "url": "https://glygen.org/publication/PubMed/12640026" } ] }, { "title": "Focal adhesion kinase signaling activities and their implications in the control of cell survival and motility.", "journal": "Frontiers in bioscience : a journal and virtual library", "date": "2003-05-01", "authors": "Hanks Steven K, Ryzhova Larisa, Shin Nah-Young, Br\u00e1bek Jan", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12700132", "url": "https://glygen.org/publication/PubMed/12700132" } ] }, { "title": "Fibronectin fragment activation of proline-rich tyrosine kinase PYK2 mediates integrin signals regulating collagenase-3 expression by human chondrocytes through a protein kinase C-dependent pathway.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Loeser RF, Forsyth CB, Samarel AM, Im HJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12730223", "url": "https://glygen.org/publication/PubMed/12730223" } ] }, { "title": "Cyclic phosphatidic acid inhibits RhoA-mediated autophosphorylation of FAK at Tyr-397 and subsequent tumor-cell invasion.", "journal": "International journal of oncology", "date": "2003-06", "authors": "Mukai Mutsuko, Iwasaki Teruo, Tatsuta Masaharu, Togawa Atsushi, Nakamura Hiroyuki, Murakami-Murofushi Kimiko, Kobayashi Susumu, Imamura Fumio, Inoue Masahiro", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12738990", "url": "https://glygen.org/publication/PubMed/12738990" } ] }, { "title": "ERK 1/2- and JNKs-dependent synthesis of interleukins 6 and 8 by fibroblast-like synoviocytes stimulated with protein I/II, a modulin from oral streptococci, requires focal adhesion kinase.", "journal": "The Journal of biological chemistry", "date": "2003-07-25", "authors": "Neff Laurence, Zeisel Mirjam, Druet Vanessa, Takeda Ken, Klein Jean-Paul, Sibilia Jean, Wachsmann Dominique", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12761229", "url": "https://glygen.org/publication/PubMed/12761229" } ] }, { "title": "FAK overexpression is correlated with tumour invasiveness and lymph node metastasis in oesophageal squamous cell carcinoma.", "journal": "British journal of cancer", "date": "2003-07-07", "authors": "Miyazaki T, Kato H, Nakajima M, Sohda M, Fukai Y, Masuda N, Manda R, Fukuchi M, Tsukada K, Kuwano H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12838315", "url": "https://glygen.org/publication/PubMed/12838315" } ] }, { "title": "Expression of GRP and its receptor in well-differentiated colon cancer cells correlates with the presence of focal adhesion kinase phosphorylated at tyrosines 397 and 407.", "journal": "The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society", "date": "2003", "authors": "Matkowskyj KA, Keller K, Glover S, Kornberg L, Tran-Son-Tay R, Benya RV", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12871985", "url": "https://glygen.org/publication/PubMed/12871985" } ] }, { "title": "PAK1 phosphorylation of MEK1 regulates fibronectin-stimulated MAPK activation.", "journal": "The Journal of cell biology", "date": "2003", "authors": "Slack-Davis JK, Eblen ST, Zecevic M, Boerner SA, Tarcsafalvi A, Diaz HB, Marshall MS, Weber MJ, Parsons JT, Catling AD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12876277", "url": "https://glygen.org/publication/PubMed/12876277" } ] }, { "title": "Absence of adhesion triggers differential FAK and SAPKp38 signals in SW620 human colon cancer cells that may inhibit adhesiveness and lead to cell death.", "journal": "Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology", "date": "2003", "authors": "Walsh MF, Thamilselvan V, Grotelueschen R, Farhana L, Basson M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12876384", "url": "https://glygen.org/publication/PubMed/12876384" } ] }, { "title": "Fibronectin enhances viability and alters cytoskeletal functions (with effects on the phosphatidylinositol 3-kinase pathway) in small cell lung cancer.", "journal": "Journal of cellular and molecular medicine", "date": "2003", "authors": "Kijima T, Maulik G, Ma PC, Madhiwala P, Schaefer E, Salgia R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054" } ] }, { "title": "A novel mode for integrin-mediated signaling: tethering is required for phosphorylation of FAK Y397.", "journal": "Molecular biology of the cell", "date": "2003", "authors": "Shi Q, Boettiger D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12960434", "url": "https://glygen.org/publication/PubMed/12960434" } ] }, { "title": "PIAS1-mediated sumoylation of focal adhesion kinase activates its autophosphorylation.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Kadare G, Toutant M, Formstecher E, Corvol JC, Carnaud M, Boutterin MC, Girault JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14500712", "url": "https://glygen.org/publication/PubMed/14500712" } ] }, { "title": "Expression of focal adhesion kinase and phosphorylated focal adhesion kinase in squamous cell carcinoma of the larynx.", "journal": "The Laryngoscope", "date": "2003-11", "authors": "Aronsohn Michael S, Brown Heather M, Hauptman Garrett, Kornberg Lori J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14603053", "url": "https://glygen.org/publication/PubMed/14603053" } ] }, { "title": "Collagen IV regulates Caco-2 migration and ERK activation via alpha1beta1- and alpha2beta1-integrin-dependent Src kinase activation.", "journal": "American journal of physiology. Gastrointestinal and liver physiology", "date": "2004", "authors": "Sanders MA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14604860", "url": "https://glygen.org/publication/PubMed/14604860" } ] }, { "title": "ROCK-generated contractility regulates breast epithelial cell differentiation in response to the physical properties of a three-dimensional collagen matrix.", "journal": "The Journal of cell biology", "date": "2003", "authors": "Wozniak MA, Desai R, Solski PA, Der CJ, Keely PJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14610060", "url": "https://glygen.org/publication/PubMed/14610060" } ] }, { "title": "Inositol hexaphosphate (IP6) inhibits key events of cancer metastasis: II. Effects on integrins and focal adhesions.", "journal": "Anticancer research", "date": "2003", "authors": "Tantivejkul Kwanchanit, Vucenik Ivana, Shamsuddin Abulkalam M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14666664", "url": "https://glygen.org/publication/PubMed/14666664" } ] }, { "title": "Degradation and dephosphorylation of focal adhesion kinase during okadaic acid-induced apoptosis in human neuroblastoma cells.", "journal": "Neoplasia (New York, N.Y.)", "date": "2003", "authors": "Kim B, van Golen CM, Feldman EL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14670178", "url": "https://glygen.org/publication/PubMed/14670178" } ] }, { "title": "Ionizing radiation modules of the expression and tyrosine phosphorylation of the focal adhesion-associated proteins focal adhesion kinase (FAK) and its substrates p130cas and paxillin in A549 human lung carcinoma cells in vitro.", "journal": "International journal of radiation biology", "date": "2003", "authors": "Beinke C, Van Beuningen D, Cordes N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14703945", "url": "https://glygen.org/publication/PubMed/14703945" } ] }, { "title": "Regulation of CXCR4-mediated chemotaxis and chemoinvasion of breast cancer cells.", "journal": "Oncogene", "date": "2004", "authors": "Fernandis AZ, Prasad A, Band H, Klosel R, Ganju RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14712221", "url": "https://glygen.org/publication/PubMed/14712221" } ] }, { "title": "Extracellular pressure stimulates macrophage phagocytosis by inhibiting a pathway involving FAK and ERK.", "journal": "American journal of physiology. Cell physiology", "date": "2004", "authors": "Shiratsuchi H, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14761895", "url": "https://glygen.org/publication/PubMed/14761895" } ] }, { "title": "Phosphorylation of focal adhesion kinase tyrosine 397 critically mediates gastrin-releasing peptide's morphogenic properties.", "journal": "Journal of cellular physiology", "date": "2004-04", "authors": "Glover Sarah, Delaney Melissa, Dematte Cecile, Kornberg Lori, Frasco Melissa, Tran-Son-Tay Roger, Benya Richard V", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14978737", "url": "https://glygen.org/publication/PubMed/14978737" } ] }, { "title": "Expression of focal adhesion kinase in acute myeloid leukemia is associated with enhanced blast migration, increased cellularity, and poor prognosis.", "journal": "Cancer research", "date": "2004", "authors": "Recher C, Ysebaert L, Beyne-Rauzy O, Mansat-De Mas V, Ruidavets JB, Cariven P, Demur C, Payrastre B, Laurent G, Racaud-Sultan C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15126359", "url": "https://glygen.org/publication/PubMed/15126359" } ] }, { "title": "Vinculin modulation of paxillin-FAK interactions regulates ERK to control survival and motility.", "journal": "The Journal of cell biology", "date": "2004", "authors": "Subauste MC, Pertz O, Adamson ED, Turner CE, Junger S, Hahn KM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15138291", "url": "https://glygen.org/publication/PubMed/15138291" } ] }, { "title": "Melanoma chondroitin sulfate proteoglycan enhances FAK and ERK activation by distinct mechanisms.", "journal": "The Journal of cell biology", "date": "2004", "authors": "Yang J, Price MA, Neudauer CL, Wilson C, Ferrone S, Xia H, Iida J, Simpson MA, McCarthy JB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15210734", "url": "https://glygen.org/publication/PubMed/15210734" } ] }, { "title": "Interaction of the disintegrin and cysteine-rich domains of ADAM12 with integrin alpha7beta1.", "journal": "Experimental cell research", "date": "2004", "authors": "Zhao Z, Gruszczynska-Biegala J, Cheuvront T, Yi H, von der Mark H, von der Mark K, Kaufman SJ, Zolkiewska A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15242759", "url": "https://glygen.org/publication/PubMed/15242759" } ] }, { "title": "Focal adhesion regulation of cell behavior.", "journal": "Biochimica et biophysica acta", "date": "2004", "authors": "Wozniak MA, Modzelewska K, Kwong L, Keely PJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15246682", "url": "https://glygen.org/publication/PubMed/15246682" } ] }, { "title": "Roles played by a subset of integrin signaling molecules in cadherin-based cell-cell adhesion.", "journal": "The Journal of cell biology", "date": "2004", "authors": "Yano H, Mazaki Y, Kurokawa K, Hanks SK, Matsuda M, Sabe H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" } ] }, { "title": "Squamous cell carcinoma cell aggregates escape suspension-induced, p53-mediated anoikis: fibronectin and integrin alphav mediate survival signals through focal adhesion kinase.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Zhang Y, Lu H, Dazin P, Kapila Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15331608", "url": "https://glygen.org/publication/PubMed/15331608" } ] }, { "title": "CrkII regulates focal adhesion kinase activation by making a complex with Crk-associated substrate, p130Cas.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Iwahara T, Akagi T, Fujitsuka Y, Hanafusa H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15598735", "url": "https://glygen.org/publication/PubMed/15598735" } ] }, { "title": "Residues within the first subdomain of the FERM-like domain in focal adhesion kinase are important in its regulation.", "journal": "The Journal of biological chemistry", "date": "2005-03-04", "authors": "Cohen Lee Ann, Guan Jun-Lin", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15611137", "url": "https://glygen.org/publication/PubMed/15611137" } ] }, { "title": "Activation of p38 MAPKalpha by extracellular pressure mediates the stimulation of macrophage phagocytosis by pressure.", "journal": "American journal of physiology. Cell physiology", "date": "2005", "authors": "Shiratsuchi H, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15625302", "url": "https://glygen.org/publication/PubMed/15625302" } ] }, { "title": "Growth factors stimulate kidney proximal tubule cell migration independent of augmented tyrosine phosphorylation of focal adhesion kinase.", "journal": "Biochemical and biophysical research communications", "date": "2005", "authors": "Cao Y, Baig MR, Hamm LL, Wu K, Simon EE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ] }, { "title": "Differential effects of shear stress and cyclic stretch on focal adhesion remodeling, site-specific FAK phosphorylation, and small GTPases in human lung endothelial cells.", "journal": "Experimental cell research", "date": "2005", "authors": "Shikata Y, Rios A, Kawkitinarong K, DePaola N, Garcia JG, Birukov KG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15707572", "url": "https://glygen.org/publication/PubMed/15707572" } ] }, { "title": "The PPFLMLLKGSTR motif in globular domain 3 of the human laminin-5 alpha3 chain is crucial for integrin alpha3beta1 binding and cell adhesion.", "journal": "Experimental cell research", "date": "2005", "authors": "Kim JM, Park WH, Min BM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15707596", "url": "https://glygen.org/publication/PubMed/15707596" } ] }, { "title": "Correlation between 99mTc-(V)-DMSA uptake and constitutive level of phosphorylated focal adhesion kinase in an in vitro model of cancer cell lines.", "journal": "European journal of nuclear medicine and molecular imaging", "date": "2005", "authors": "Denoyer D, Perek N, Le Jeune N, Cornillon J, Dubois F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15785954", "url": "https://glygen.org/publication/PubMed/15785954" } ] }, { "title": "In situ photoactivation of a caged phosphotyrosine peptide derived from focal adhesion kinase temporarily halts lamellar extension of single migrating tumor cells.", "journal": "The Journal of biological chemistry", "date": "2005-06-10", "authors": "Humphrey David, Rajfur Zenon, Vazquez M Eugenio, Scheswohl Danielle, Schaller Michael D, Jacobson Ken, Imperiali Barbara", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15817454", "url": "https://glygen.org/publication/PubMed/15817454" } ] }, { "title": "Differentiation of C2C12 myoblasts is critically regulated by FAK signaling.", "journal": "American journal of physiology. Regulatory, integrative and comparative physiology", "date": "2005-09", "authors": "Clemente Carolina F M Z, Corat Marcus A F, Saad Sara T O, Franchini Kleber G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15890789", "url": "https://glygen.org/publication/PubMed/15890789" } ] }, { "title": "Activation of focal adhesion kinase in human lung cancer cells involves multiple and potentially parallel signaling events.", "journal": "Journal of cellular and molecular medicine", "date": "2005", "authors": "Mukhopadhyay Nishit K, Gordon Gavin J, Chen Chang-Jie, Bueno Raphael, Sugarbaker David J, Jaklitsch Michael T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15963258", "url": "https://glygen.org/publication/PubMed/15963258" } ] }, { "title": "A truncated FAK lacking the FERM domain displays high catalytic activity but retains responsiveness to adhesion-mediated signals.", "journal": "Biochemical and biophysical research communications", "date": "2005", "authors": "Jacamo RO, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16039608", "url": "https://glygen.org/publication/PubMed/16039608" } ] }, { "title": "Direct phosphorylation of proliferative and survival pathway proteins by RET.", "journal": "Surgery", "date": "2005", "authors": "Panta GR, Du L, Nwariaku FE, Kim LT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" } ] }, { "title": "Regulation of focal adhesion dynamics and disassembly by phosphorylation of FAK at tyrosine 397.", "journal": "Journal of cell science", "date": "2005", "authors": "Hamadi A, Bouali M, Dontenwill M, Stoeckel H, Takeda K, Ronde P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16159962", "url": "https://glygen.org/publication/PubMed/16159962" } ] }, { "title": "Role of focal adhesion kinase in flow-induced dilation of coronary arterioles.", "journal": "Arteriosclerosis, thrombosis, and vascular biology", "date": "2005", "authors": "Koshida R, Rocic P, Saito S, Kiyooka T, Zhang C, Chilian WM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16195476", "url": "https://glygen.org/publication/PubMed/16195476" } ] }, { "title": "Minimal features of paxillin that are required for the tyrosine phosphorylation of focal adhesion kinase.", "journal": "The Biochemical journal", "date": "2006-01-15", "authors": "Wade Ramon, Vande Pol Scott", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16253116", "url": "https://glygen.org/publication/PubMed/16253116" } ] }, { "title": "Focal adhesion kinase promotes the aggressive melanoma phenotype.", "journal": "Cancer research", "date": "2005", "authors": "Hess AR, Postovit LM, Margaryan NV, Seftor EA, Schneider GB, Seftor RE, Nickoloff BJ, Hendrix MJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16267008", "url": "https://glygen.org/publication/PubMed/16267008" } ] }, { "title": "FAK signaling is critical for ErbB-2/ErbB-3 receptor cooperation for oncogenic transformation and invasion.", "journal": "The Journal of cell biology", "date": "2005-11-07", "authors": "Benlimame Naciba, He Qiang, Jie Su, Xiao Dingzhang, Xu Ying Jie, Loignon Martin, Schlaepfer David D, Alaoui-Jamali Moulay A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754" } ] }, { "title": "The microtubule binding drug laulimalide inhibits vascular endothelial growth factor-induced human endothelial cell migration and is synergistic when combined with docetaxel (taxotere).", "journal": "Molecular pharmacology", "date": "2006", "authors": "Lu H, Murtagh J, Schwartz EL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16415178", "url": "https://glygen.org/publication/PubMed/16415178" } ] }, { "title": "Integrin alpha2-mediated ERK and calpain activation play a critical role in cell adhesion and motility via focal adhesion kinase signaling: identification of a novel signaling pathway.", "journal": "The Journal of biological chemistry", "date": "2006-03-31", "authors": "Sawhney Rajinder S, Cookson Michelle M, Omar Yasin, Hauser Jennie, Brattain Michael G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16461767", "url": "https://glygen.org/publication/PubMed/16461767" } ] }, { "title": "Membrane-type 1 matrix metalloproteinase modulates focal adhesion stability and cell migration.", "journal": "Experimental cell research", "date": "2006", "authors": "Takino T, Watanabe Y, Matsui M, Miyamori H, Kudo T, Seiki M, Sato H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16473349", "url": "https://glygen.org/publication/PubMed/16473349" } ] }, { "title": "Role of Src-specific phosphorylation site on focal adhesion kinase for senescence-associated apoptosis resistance.", "journal": "Apoptosis : an international journal on programmed cell death", "date": "2006", "authors": "Ryu SJ, Cho KA, Oh YS, Park SC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16523241", "url": "https://glygen.org/publication/PubMed/16523241" } ] }, { "title": "Reduced expression of focal adhesion kinase disrupts insulin action in skeletal muscle cells.", "journal": "Endocrinology", "date": "2006", "authors": "Huang D, Khoe M, Ilic D, Bryer-Ash M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16574795", "url": "https://glygen.org/publication/PubMed/16574795" } ] }, { "title": "Role of c-Src in human MCF7 breast cancer cell tumorigenesis.", "journal": "The Journal of biological chemistry", "date": "2006", "authors": "Gonzalez L, Agullo-Ortuno MT, Garcia-Martinez JM, Calcabrini A, Gamallo C, Palacios J, Aranda A, Martin-Perez J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16728403", "url": "https://glygen.org/publication/PubMed/16728403" } ] }, { "title": "An inhibitory role for FAK in regulating proliferation: a link between limited adhesion and RhoA-ROCK signaling.", "journal": "The Journal of cell biology", "date": "2006-07-17", "authors": "Pirone Dana M, Liu Wendy F, Ruiz Sami Alom, Gao Lin, Raghavan Srivatsan, Lemmon Christopher A, Romer Lewis H, Chen Christopher S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16847103", "url": "https://glygen.org/publication/PubMed/16847103" } ] }, { "title": "Role of focal adhesion kinase and phosphatidylinositol 3'-kinase in integrin fibronectin receptor-mediated, matrix metalloproteinase-1-dependent invasion by metastatic prostate cancer cells.", "journal": "Cancer research", "date": "2006", "authors": "Zeng ZZ, Jia Y, Hahn NJ, Markwart SM, Rockwood KF, Livant DL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16912186", "url": "https://glygen.org/publication/PubMed/16912186" } ] }, { "title": "Integrin alpha3beta1-dependent activation of FAK/Src regulates Rac1-mediated keratinocyte polarization on laminin-5.", "journal": "The Journal of investigative dermatology", "date": "2007", "authors": "Choma DP, Milano V, Pumiglia KM, DiPersio CM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494" } ] }, { "title": "Deoxycholic acid differentially regulates focal adhesion kinase phosphorylation: role of tyrosine phosphatase ShP2.", "journal": "American journal of physiology. Gastrointestinal and liver physiology", "date": "2006", "authors": "Khare S, Holgren C, Samarel AM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16920701", "url": "https://glygen.org/publication/PubMed/16920701" } ] }, { "title": "Enhanced expression of cholecystokinin-2 receptor promotes the progression of colon cancer through activation of focal adhesion kinase.", "journal": "International journal of cancer", "date": "2006", "authors": "Yu HG, Tong SL, Ding YM, Ding J, Fang XM, Zhang XF, Liu ZJ, Zhou YH, Liu QS, Luo HS, Yu JP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16998832", "url": "https://glygen.org/publication/PubMed/16998832" } ] }, { "title": "Focal adhesion kinase signaling pathways regulate the osteogenic differentiation of human mesenchymal stem cells.", "journal": "Experimental cell research", "date": "2007", "authors": "Salasznyk RM, Klees RF, Williams WA, Boskey A, Plopper GE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17081517", "url": "https://glygen.org/publication/PubMed/17081517" } ] }, { "title": "Repetitive deformation activates focal adhesion kinase and ERK mitogenic signals in human Caco-2 intestinal epithelial cells through Src and Rac1.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Chaturvedi LS, Marsh HM, Shang X, Zheng Y, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17088251", "url": "https://glygen.org/publication/PubMed/17088251" } ] }, { "title": "FAK phosphorylation at Ser-843 inhibits Tyr-397 phosphorylation, cell spreading and migration.", "journal": "Journal of cellular physiology", "date": "2007-02", "authors": "Jacamo Rodrigo, Jiang Xiaohua, Lunn J Adrian, Rozengurt Enrique", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17096371", "url": "https://glygen.org/publication/PubMed/17096371" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] }, { "title": "Src and focal adhesion kinase mediate mechanical strain-induced proliferation and ERK1/2 phosphorylation in human H441 pulmonary epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2007", "authors": "Chaturvedi LS, Marsh HM, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17215324", "url": "https://glygen.org/publication/PubMed/17215324" } ] }, { "title": "A novel low-molecular weight inhibitor of focal adhesion kinase, TAE226, inhibits glioma growth.", "journal": "Molecular carcinogenesis", "date": "2007", "authors": "Shi Q, Hjelmeland AB, Keir ST, Song L, Wickman S, Jackson D, Ohmori O, Bigner DD, Friedman HS, Rich JN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439" } ] }, { "title": "PRL-1 tyrosine phosphatase regulates c-Src levels, adherence, and invasion in human lung cancer cells.", "journal": "Cancer research", "date": "2007", "authors": "Achiwa H, Lazo JS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17234774", "url": "https://glygen.org/publication/PubMed/17234774" } ] }, { "title": "Bortezomib inhibits cell-cell adhesion and cell migration and enhances epidermal growth factor receptor inhibitor-induced cell death in squamous cell cancer.", "journal": "Cancer research", "date": "2007", "authors": "Lorch JH, Thomas TO, Schmoll HJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17234784", "url": "https://glygen.org/publication/PubMed/17234784" } ] }, { "title": "Differential FAK phosphorylation at Ser-910, Ser-843 and Tyr-397 induced by angiotensin II, LPA and EGF in intestinal epithelial cells.", "journal": "Cellular signalling", "date": "2007", "authors": "Jiang X, Sinnett-Smith J, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116" } ] }, { "title": "Cellular characterization of a novel focal adhesion kinase inhibitor.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Slack-Davis JK, Martin KH, Tilghman RW, Iwanicki M, Ung EJ, Autry C, Luzzio MJ, Cooper B, Kath JC, Roberts WG, Parsons JT", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17395594", "url": "https://glygen.org/publication/PubMed/17395594" } ] }, { "title": "Inhibition of both focal adhesion kinase and insulin-like growth factor-I receptor kinase suppresses glioma proliferation in vitro and in vivo.", "journal": "Molecular cancer therapeutics", "date": "2007", "authors": "Liu TJ, LaFortune T, Honda T, Ohmori O, Hatakeyama S, Meyer T, Jackson D, de Groot J, Yung WK", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17431114", "url": "https://glygen.org/publication/PubMed/17431114" } ] }, { "title": "Increased expression and phosphorylation of focal adhesion kinase correlates with dysfunction in the volume-overloaded human heart.", "journal": "Clinical science (London, England : 1979)", "date": "2007", "authors": "Lopes MM, Ribeiro GC, Tornatore TF, Clemente CF, Teixeira VP, Franchini KG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17497960", "url": "https://glygen.org/publication/PubMed/17497960" } ] }, { "title": "Transient forebrain ischemia effects FAK-coupled signaling in gerbil hippocampus.", "journal": "Neurochemistry international", "date": "2007", "authors": "Ziemka-Nalecz M, Zalewska T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17524523", "url": "https://glygen.org/publication/PubMed/17524523" } ] }, { "title": "Focal adhesion kinase controls actin assembly via a FERM-mediated interaction with the Arp2/3 complex.", "journal": "Nature cell biology", "date": "2007-09", "authors": "Serrels Bryan, Serrels Alan, Brunton Valerie G, Holt Mark, McLean Gordon W, Gray Christopher H, Jones Gareth E, Frame Margaret C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17721515", "url": "https://glygen.org/publication/PubMed/17721515" } ] }, { "title": "Alpha-actinin-1 phosphorylation modulates pressure-induced colon cancer cell adhesion through regulation of focal adhesion kinase-Src interaction.", "journal": "American journal of physiology. Cell physiology", "date": "2007", "authors": "Craig DH, Haimovich B, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17898132", "url": "https://glygen.org/publication/PubMed/17898132" } ] }, { "title": "Therapeutic efficacy of a novel focal adhesion kinase inhibitor TAE226 in ovarian carcinoma.", "journal": "Cancer research", "date": "2007", "authors": "Halder J, Lin YG, Merritt WM, Spannuth WA, Nick AM, Honda T, Kamat AA, Han LY, Kim TJ, Lu C, Tari AM, Bornmann W, Fernandez A, Lopez-Berestein G, Sood AK", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18006843", "url": "https://glygen.org/publication/PubMed/18006843" } ] }, { "title": "MAP-kinase activity necessary for TGFbeta1-stimulated mesangial cell type I collagen expression requires adhesion-dependent phosphorylation of FAK tyrosine 397.", "journal": "Journal of cell science", "date": "2007", "authors": "Hayashida T, Wu MH, Pierce A, Poncelet AC, Varga J, Schnaper HW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18032789", "url": "https://glygen.org/publication/PubMed/18032789" } ] }, { "title": "Multiple paxillin binding sites regulate FAK function.", "journal": "Journal of molecular signaling", "date": "2008", "authors": "Scheswohl DM, Harrell JR, Rajfur Z, Gao G, Campbell SL, Schaller MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" } ] }, { "title": "Tac-beta1 inhibits FAK activation and Src signaling.", "journal": "Biochemical and biophysical research communications", "date": "2008", "authors": "Berrier AL, Jones CW, LaFlamme SE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18198129", "url": "https://glygen.org/publication/PubMed/18198129" } ] }, { "title": "Troglitazone inhibits cell migration, adhesion, and spreading by modulating cytoskeletal rearrangement in human breast cancer cells.", "journal": "Molecular carcinogenesis", "date": "2008", "authors": "Wang PS, Chou FS, Porchia L, Saji M, Pinzone JJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18314876", "url": "https://glygen.org/publication/PubMed/18314876" } ] }, { "title": "Inhibitory role of focal adhesion kinase on anoikis in the lung cancer cell A549.", "journal": "Cell biology international", "date": "2008", "authors": "Liu G, Meng X, Jin Y, Bai J, Zhao Y, Cui X, Chen F, Fu S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694" } ] }, { "title": "Involvement of focal adhesion kinase in cellular invasion of head and neck squamous cell carcinomas via regulation of MMP-2 expression.", "journal": "British journal of cancer", "date": "2008-04-08", "authors": "Canel M, Secades P, Garz\u00f3n-Arango M, Allonca E, Suarez C, Serrels A, Frame Mc, Brunton V, Chiara M-D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846" } ] }, { "title": "FAK/src-family dependent activation of the Ste20-like kinase SLK is required for microtubule-dependent focal adhesion turnover and cell migration.", "journal": "PloS one", "date": "2008", "authors": "Wagner S, Storbeck CJ, Roovers K, Chaar ZY, Kolodziej P, McKay M, Sabourin LA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18382658", "url": "https://glygen.org/publication/PubMed/18382658" } ] }, { "title": "Focal adhesion kinase is not required for Src-induced formation of invadopodia in KM12C colon cancer cells and can interfere with their assembly.", "journal": "European journal of cell biology", "date": "2008", "authors": "Vitale S, Avizienyte E, Brunton VG, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18562041", "url": "https://glygen.org/publication/PubMed/18562041" } ] }, { "title": "Neutrophil gelatinase-associated lipocalin: a novel suppressor of invasion and angiogenesis in pancreatic cancer.", "journal": "Cancer research", "date": "2008", "authors": "Tong Z, Kunnumakkara AB, Wang H, Matsuo Y, Diagaradjane P, Harikumar KB, Ramachandran V, Sung B, Chakraborty A, Bresalier RS, Logsdon C, Aggarwal BB, Krishnan S, Guha S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18676832", "url": "https://glygen.org/publication/PubMed/18676832" } ] }, { "title": "Shp2 negatively regulates growth in cardiomyocytes by controlling focal adhesion kinase/Src and mTOR pathways.", "journal": "Circulation research", "date": "2008-10-10", "authors": "Marin Talita M, Clemente Carolina F M Z, Santos Aline M, Picardi Paty K, Pascoal Vin\u00edcius D B, Lopes-Cendes Iscia, Saad M\u00e1rio J A, Franchini Kleber G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18757826", "url": "https://glygen.org/publication/PubMed/18757826" } ] }, { "title": "ADAM15 modulates outside-in signalling in chondrocyte-matrix interactions.", "journal": "Journal of cellular and molecular medicine", "date": "2009", "authors": "Bohm BB, Schirner A, Burkhardt H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18774960", "url": "https://glygen.org/publication/PubMed/18774960" } ] }, { "title": "Early adhesion induces interaction of FAK and Fyn in lipid domains and activates raft-dependent Akt signaling in SW480 colon cancer cells.", "journal": "Biochimica et biophysica acta", "date": "2008", "authors": "Baillat G, Siret C, Delamarre E, Luis J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444" } ] }, { "title": "beta1-integrin mediates myelin-associated glycoprotein signaling in neuronal growth cones.", "journal": "Molecular brain", "date": "2008", "authors": "Goh EL, Young JK, Kuwako K, Tessier-Lavigne M, He Z, Griffin JW, Ming GL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18922173", "url": "https://glygen.org/publication/PubMed/18922173" } ] }, { "title": "Mechanosensing machinery for cells under low substratum rigidity.", "journal": "American journal of physiology. Cell physiology", "date": "2008", "authors": "Wei WC, Lin HH, Shen MR, Tang MJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18923058", "url": "https://glygen.org/publication/PubMed/18923058" } ] }, { "title": "Interaction of Xiphophorus and murine Fyn with focal adhesion kinase.", "journal": "Comparative biochemistry and physiology. Toxicology & pharmacology : CBP", "date": "2009-03", "authors": "Teutschbein Janka, Schartl Manfred, Meierjohann Svenja", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18930841", "url": "https://glygen.org/publication/PubMed/18930841" } ] }, { "title": "A small molecule inhibitor, 1,2,4,5-benzenetetraamine tetrahydrochloride, targeting the y397 site of focal adhesion kinase decreases tumor growth.", "journal": "Journal of medicinal chemistry", "date": "2008", "authors": "Golubovskaya VM, Nyberg C, Zheng M, Kweh F, Magis A, Ostrov D, Cance WG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18989950", "url": "https://glygen.org/publication/PubMed/18989950" } ] }, { "title": "The lysyl oxidase pro-peptide attenuates fibronectin-mediated activation of focal adhesion kinase and p130Cas in breast cancer cells.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Zhao Y, Min C, Vora SR, Trackman PC, Sonenshein GE, Kirsch KH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19029090", "url": "https://glygen.org/publication/PubMed/19029090" } ] }, { "title": "Regulation of focal adhesion turnover by ErbB signalling in invasive breast cancer cells.", "journal": "British journal of cancer", "date": "2009-02-24", "authors": "Xu Y, Benlimame N, Su J, He Q, Alaoui-Jamali M A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626" } ] }, { "title": "The integrin antagonist cilengitide activates alphaVbeta3, disrupts VE-cadherin localization at cell junctions and enhances permeability in endothelial cells.", "journal": "PloS one", "date": "2009", "authors": "Alghisi GC, Ponsonnet L, Ruegg C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436" } ] }, { "title": "Fibronectin promotes invasiveness and focal adhesion kinase tyrosine phosphorylation of human colon cancer cell.", "journal": "Hepato-gastroenterology", "date": "2008", "authors": "Ding J, Li D, Wang X, Wang C, Wu T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19260479", "url": "https://glygen.org/publication/PubMed/19260479" } ] }, { "title": "Mechano-transduction to muscle protein synthesis is modulated by FAK.", "journal": "European journal of applied physiology", "date": "2009", "authors": "Klossner S, Durieux AC, Freyssenet D, Flueck M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19294408", "url": "https://glygen.org/publication/PubMed/19294408" } ] }, { "title": "Focal adhesion kinase modulates cell adhesion strengthening via integrin activation.", "journal": "Molecular biology of the cell", "date": "2009-05", "authors": "Michael Kristin E, Dumbauld David W, Burns Kellie L, Hanks Steven K, Garc\u00eda Andr\u00e9s J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19297531", "url": "https://glygen.org/publication/PubMed/19297531" } ] }, { "title": "Focal adhesion kinase acts downstream of EphB receptors to maintain mature dendritic spines by regulating cofilin activity.", "journal": "The Journal of neuroscience : the official journal of the Society for Neuroscience", "date": "2009", "authors": "Shi Y, Pontrello CG, DeFea KA, Reichardt LF, Ethell IM", "evidence": [ { "database": "Reactome", "id": "R-HSA-3928662", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-3928662" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19553453", "url": "https://glygen.org/publication/PubMed/19553453" } ] }, { "title": "Characterisation of fibronectin-mediated FAK signalling pathways in lung cancer cell migration and invasion.", "journal": "British journal of cancer", "date": "2009", "authors": "Meng XN, Jin Y, Yu Y, Bai J, Liu GY, Zhu J, Zhao YZ, Wang Z, Chen F, Lee KY, Fu SB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240" } ] }, { "title": "Endothelial barrier protection by FTY720 under hyperglycemic condition: involvement of focal adhesion kinase, small GTPases, and adherens junction proteins.", "journal": "American journal of physiology. Cell physiology", "date": "2009", "authors": "Sarai K, Shikata K, Shikata Y, Omori K, Watanabe N, Sasaki M, Nishishita S, Wada J, Goda N, Kataoka N, Makino H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053" } ] }, { "title": "The direct effect of focal adhesion kinase (FAK), dominant-negative FAK, FAK-CD and FAK siRNA on gene expression and human MCF-7 breast cancer cell tumorigenesis.", "journal": "BMC cancer", "date": "2009", "authors": "Golubovskaya VM, Zheng M, Zhang L, Li JL, Cance WG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19671193", "url": "https://glygen.org/publication/PubMed/19671193" } ] }, { "title": "Periostin mediates vascular smooth muscle cell migration through the integrins alphavbeta3 and alphavbeta5 and focal adhesion kinase (FAK) pathway.", "journal": "Atherosclerosis", "date": "2010", "authors": "Li G, Jin R, Norris RA, Zhang L, Yu S, Wu F, Markwald RR, Nanda A, Conway SJ, Smyth SS, Granger DN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19695571", "url": "https://glygen.org/publication/PubMed/19695571" } ] }, { "title": "Therapeutic targeting of the focal adhesion complex prevents oncogenic TGF-beta signaling and metastasis.", "journal": "Breast cancer research : BCR", "date": "2009", "authors": "Wendt MK, Schiemann WP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433" } ] }, { "title": "STEAP4 regulates focal adhesion kinase activation and CpG motifs within STEAP4 promoter region are frequently methylated in DU145, human androgen-independent prostate cancer cells.", "journal": "Int. J. Mol. Med.", "date": "2009", "authors": "Tamura T, Chiba J", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19787193", "url": "https://glygen.org/publication/PubMed/19787193" } ] }, { "title": "Matrix density-induced mechanoregulation of breast cell phenotype, signaling and gene expression through a FAK-ERK linkage.", "journal": "Oncogene", "date": "2009", "authors": "Provenzano PP, Inman DR, Eliceiri KW, Keely PJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19826415", "url": "https://glygen.org/publication/PubMed/19826415" } ] }, { "title": "Stretch activates human myometrium via ERK, caldesmon and focal adhesion signaling.", "journal": "PloS one", "date": "2009", "authors": "Li Y, Reznichenko M, Tribe RM, Hess PE, Taggart M, Kim H, DeGnore JP, Gangopadhyay S, Morgan KG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19834610", "url": "https://glygen.org/publication/PubMed/19834610" } ] }, { "title": "Focal adhesion kinase-dependent regulation of adhesive forces involves vinculin recruitment to focal adhesions.", "journal": "Biology of the cell", "date": "2010-01-14", "authors": "Dumbauld David W, Michael Kristin E, Hanks Steven K, Garc\u00eda Andr\u00e9s J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375" } ] }, { "title": "Abnormalities in focal adhesion complex formation, regulation, and function in human autosomal recessive polycystic kidney disease epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2010", "authors": "Israeli S, Amsler K, Zheleznova N, Wilson PD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" } ] }, { "title": "Oleic acid promotes migration on MDA-MB-231 breast cancer cells through an arachidonic acid-dependent pathway.", "journal": "The international journal of biochemistry & cell biology", "date": "2010", "authors": "Navarro-Tito N, Soto-Guzman A, Castro-Sanchez L, Martinez-Orozco R, Salazar EP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19931412", "url": "https://glygen.org/publication/PubMed/19931412" } ] }, { "title": "Progress in researches about focal adhesion kinase in gastrointestinal tract.", "journal": "World journal of gastroenterology", "date": "2009-12-21", "authors": "Hao Hui-Fang, Naomoto Yoshio, Bao Xiao-Hong, Watanabe Nobuyuki, Sakurama Kazufumi, Noma Kazuhiro, Tomono Yasuko, Fukazawa Takuya, Shirakawa Yasuhiro, Yamatsuji Tomoki, Matsuoka Junji, Takaoka Munenori", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455" } ] }, { "title": "JNK pathway-associated phosphatase dephosphorylates focal adhesion kinase and suppresses cell migration.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Li JP, Fu YN, Chen YR, Tan TH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849" } ] }, { "title": "Intrinsic chemoresistance to gemcitabine is associated with constitutive and laminin-induced phosphorylation of FAK in pancreatic cancer cell lines.", "journal": "Molecular cancer", "date": "2009", "authors": "Huanwen W, Zhiyong L, Xiaohua S, Xinyu R, Kai W, Tonghua L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20021699", "url": "https://glygen.org/publication/PubMed/20021699" } ] }, { "title": "Grp78 promotes the invasion of hepatocellular carcinoma.", "journal": "BMC cancer", "date": "2010", "authors": "Su R, Li Z, Li H, Song H, Bao C, Wei J, Cheng L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20082722", "url": "https://glygen.org/publication/PubMed/20082722" } ] }, { "title": "Cell surface receptor-specific scaffold requirements for adhesion to laminin-derived peptide-chitosan membranes.", "journal": "Biomaterials", "date": "2010", "authors": "Hozumi K, Otagiri D, Yamada Y, Sasaki A, Fujimori C, Wakai Y, Uchida T, Katagiri F, Kikkawa Y, Nomizu M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20122724", "url": "https://glygen.org/publication/PubMed/20122724" } ] }, { "title": "Inhibition of focal adhesion kinase decreases tumor growth in human neuroblastoma.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2010", "authors": "Beierle EA, Ma X, Stewart J, Nyberg C, Trujillo A, Cance WG, Golubovskaya VM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20160475", "url": "https://glygen.org/publication/PubMed/20160475" } ] }, { "title": "FAK is involved in invasion and metastasis of hepatocellular carcinoma.", "journal": "Clinical & experimental metastasis", "date": "2010", "authors": "Chen JS, Huang XH, Wang Q, Chen XL, Fu XH, Tan HX, Zhang LJ, Li W, Bi J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20180147", "url": "https://glygen.org/publication/PubMed/20180147" } ] }, { "title": "The RGD domain of human osteopontin promotes tumor growth and metastasis through activation of survival pathways.", "journal": "PloS one", "date": "2010", "authors": "Courter D, Cao H, Kwok S, Kong C, Banh A, Kuo P, Bouley DM, Vice C, Brustugun OT, Denko NC, Koong AC, Giaccia A, Le QT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20224789", "url": "https://glygen.org/publication/PubMed/20224789" } ] }, { "title": "Myosin II activity regulates vinculin recruitment to focal adhesions through FAK-mediated paxillin phosphorylation.", "journal": "The Journal of cell biology", "date": "2010", "authors": "Pasapera AM, Schneider IC, Rericha E, Schlaepfer DD, Waterman CM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20308429", "url": "https://glygen.org/publication/PubMed/20308429" } ] }, { "title": "Inhibition of focal adhesion kinase suppresses the adverse phenotype of endocrine-resistant breast cancer cells and improves endocrine response in endocrine-sensitive cells.", "journal": "Breast cancer research and treatment", "date": "2011", "authors": "Hiscox S, Barnfather P, Hayes E, Bramble P, Christensen J, Nicholson RI, Barrett-Lee P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20354780", "url": "https://glygen.org/publication/PubMed/20354780" } ] }, { "title": "Keratin 8/18 modulation of protein kinase C-mediated integrin-dependent adhesion and migration of liver epithelial cells.", "journal": "Molecular biology of the cell", "date": "2010", "authors": "Bordeleau F, Galarneau L, Gilbert S, Loranger A, Marceau N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20357007", "url": "https://glygen.org/publication/PubMed/20357007" } ] }, { "title": "Hydrogen peroxide activates focal adhesion kinase and c-Src by a phosphatidylinositol 3 kinase-dependent mechanism and promotes cell migration in Caco-2 cell monolayers.", "journal": "American journal of physiology. Gastrointestinal and liver physiology", "date": "2010", "authors": "Basuroy S, Dunagan M, Sheth P, Seth A, Rao RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826" } ] }, { "title": "The mechanisms underlying fibroblast apoptosis regulated by growth factors during wound healing.", "journal": "The Journal of pathology", "date": "2010", "authors": "Akasaka Y, Ono I, Kamiya T, Ishikawa Y, Kinoshita T, Ishiguro S, Yokoo T, Imaizumi R, Inomata N, Fujita K, Akishima-Fukasawa Y, Uzuki M, Ito K, Ishii T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20527022", "url": "https://glygen.org/publication/PubMed/20527022" } ] }, { "title": "Expression of focal adhesion kinase and phosphorylated focal adhesion kinase in human gliomas is associated with unfavorable overall survival.", "journal": "Translational research : the journal of laboratory and clinical medicine", "date": "2010", "authors": "Ding L, Sun X, You Y, Liu N, Fu Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20621036", "url": "https://glygen.org/publication/PubMed/20621036" } ] }, { "title": "Synthetic heparan sulfate oligosaccharides inhibit endothelial cell functions essential for angiogenesis.", "journal": "PloS one", "date": "2010", "authors": "Cole CL, Hansen SU, Barath M, Rushton G, Gardiner JM, Avizienyte E, Jayson GC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20657775", "url": "https://glygen.org/publication/PubMed/20657775" } ] }, { "title": "Maspin regulates endothelial cell adhesion and migration through an integrin signaling pathway.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Qin L, Zhang M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20713357", "url": "https://glygen.org/publication/PubMed/20713357" } ] }, { "title": "Phosphorylation of focal adhesion kinase at Tyr397 in gastric carcinomas and its clinical significance.", "journal": "The American journal of pathology", "date": "2010", "authors": "Lai IR, Chu PY, Lin HS, Liou JY, Jan YJ, Lee JC, Shen TL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20724588", "url": "https://glygen.org/publication/PubMed/20724588" } ] }, { "title": "DNA copy number aberrations in small-cell lung cancer reveal activation of the focal adhesion pathway.", "journal": "Oncogene", "date": "2010-12-02", "authors": "Ocak S, Yamashita H, Udyavar A R, Miller A N, Gonzalez A L, Zou Y, Jiang A, Yi Y, Shyr Y, Estrada L, Quaranta V, Massion P P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20802517", "url": "https://glygen.org/publication/PubMed/20802517" } ] }, { "title": "Hyperphosphorylated FAK Delocalizes from Focal Adhesions to Membrane Ruffles.", "journal": "Journal of oncology", "date": "2010", "authors": "Hamadi A, Deramaudt TB, Takeda K, Ronde P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20847951", "url": "https://glygen.org/publication/PubMed/20847951" } ] }, { "title": "The role of the focal adhesion protein PINCH1 for the radiosensitivity of adhesion and suspension cell cultures.", "journal": "PloS one", "date": "2010", "authors": "Sandfort V, Eke I, Cordes N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395" } ] }, { "title": "Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line.", "journal": "Molecular cancer", "date": "2010", "authors": "Caccia D, Micciche F, Cassinelli G, Mondellini P, Casalini P, Bongarzone I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" } ] }, { "title": "The effect of lysophosphatidic acid and Rho-associated kinase patterning on adhesion of dental pulp cells.", "journal": "International endodontic journal", "date": "2011", "authors": "Cheng R, Shao MY, Yang H, Cheng L, Wang FM, Zhou XD, Hu T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21073482", "url": "https://glygen.org/publication/PubMed/21073482" } ] }, { "title": "ILK mediates the effects of strain on intestinal epithelial wound closure.", "journal": "American journal of physiology. Cell physiology", "date": "2011", "authors": "Yuan L, Sanders MA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641" } ] }, { "title": "Ligand-independent activation of c-Met by fibronectin and \u03b1(5)\u03b2(1)-integrin regulates ovarian cancer invasion and metastasis.", "journal": "Oncogene", "date": "2011-03-31", "authors": "Mitra A K, Sawada K, Tiwari P, Mui K, Gwin K, Lengyel E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21119598", "url": "https://glygen.org/publication/PubMed/21119598" } ] }, { "title": "Akt directly regulates focal adhesion kinase through association and serine phosphorylation: implication for pressure-induced colon cancer metastasis.", "journal": "American journal of physiology. Cell physiology", "date": "2011", "authors": "Wang S, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21209368", "url": "https://glygen.org/publication/PubMed/21209368" } ] }, { "title": "A peptide corresponding to the C-terminal region of pleiotrophin inhibits angiogenesis in vivo and in vitro.", "journal": "Journal of cellular biochemistry", "date": "2011", "authors": "Mikelis C, Lamprou M, Koutsioumpa M, Koutsioubas AG, Spyranti Z, Zompra AA, Spiliopoulos N, Vradis AA, Katsoris P, Spyroulias GA, Cordopatis P, Courty J, Papadimitriou E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21344482", "url": "https://glygen.org/publication/PubMed/21344482" } ] }, { "title": "Androgen-induced cell migration: role of androgen receptor/filamin A association.", "journal": "PloS one", "date": "2011", "authors": "Castoria G, D'Amato L, Ciociola A, Giovannelli P, Giraldi T, Sepe L, Paolella G, Barone MV, Migliaccio A, Auricchio F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21359179", "url": "https://glygen.org/publication/PubMed/21359179" } ] }, { "title": "Effect of focal adhesion kinase on the regulation of realignment and tenogenic differentiation of human mesenchymal stem cells by mechanical stretch.", "journal": "Connective tissue research", "date": "2011", "authors": "Xu B, Song G, Ju Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21401419", "url": "https://glygen.org/publication/PubMed/21401419" } ] }, { "title": "HAMLET binding to alpha-actinin facilitates tumor cell detachment.", "journal": "PloS one", "date": "2011", "authors": "Trulsson M, Yu H, Gisselsson L, Chao Y, Urbano A, Aits S, Mossberg AK, Svanborg C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21408150", "url": "https://glygen.org/publication/PubMed/21408150" } ] }, { "title": "Progesterone enhances vascular endothelial cell migration via activation of focal adhesion kinase.", "journal": "Journal of cellular and molecular medicine", "date": "2012", "authors": "Zheng S, Huang J, Zhou K, Xiang Q, Zhang Y, Tan Z, Simoncini T, Fu X, Wang T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517" } ] }, { "title": "Delayed caspase-8 activation and enhanced integrin beta1-activated FAK underpins anoikis in oesophageal carcinoma cells harbouring mt p53-R175H.", "journal": "Cell biology international", "date": "2011", "authors": "Fanucchi S, Veale RB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21426305", "url": "https://glygen.org/publication/PubMed/21426305" } ] }, { "title": "Chronic mechanical stress induces mucin 5AC expression in human bronchial epithelial cells through ERK dependent pathways.", "journal": "Molecular biology reports", "date": "2012", "authors": "Li N, Li Q, Zhou XD, Kolosov VP, Perelman JM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21556755", "url": "https://glygen.org/publication/PubMed/21556755" } ] }, { "title": "EGF-induced ERK-activation downstream of FAK requires rac1-NADPH oxidase.", "journal": "Journal of cellular physiology", "date": "2011", "authors": "Flinder LI, Timofeeva OA, Rosseland CM, Wierod L, Huitfeldt HS, Skarpen E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21660950", "url": "https://glygen.org/publication/PubMed/21660950" } ] }, { "title": "Suppression of E-cadherin function drives the early stages of Ras-induced squamous cell carcinoma through upregulation of FAK and Src.", "journal": "The Journal of investigative dermatology", "date": "2011", "authors": "Alt-Holland A, Sowalsky AG, Szwec-Levin Y, Shamis Y, Hatch H, Feig LA, Garlick JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" } ] }, { "title": "Endothelial cell-specific molecule 2 (ECSM2) localizes to cell-cell junctions and modulates bFGF-directed cell migration via the ERK-FAK pathway.", "journal": "PloS one", "date": "2011", "authors": "Shi C, Lu J, Wu W, Ma F, Georges J, Huang H, Balducci J, Chang Y, Huang Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547" } ] }, { "title": "FAK regulates intestinal epithelial cell survival and proliferation during mucosal wound healing.", "journal": "PloS one", "date": "2011", "authors": "Owen Katherine A, Abshire Michelle Y, Tilghman Robert W, Casanova James E, Bouton Amy H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21887232", "url": "https://glygen.org/publication/PubMed/21887232" } ] }, { "title": "RhoA/ROCK, cytoskeletal dynamics, and focal adhesion kinase are required for mechanical stretch-induced tenogenic differentiation of human mesenchymal stem cells.", "journal": "Journal of cellular physiology", "date": "2012", "authors": "Xu B, Song G, Ju Y, Li X, Song Y, Watanabe S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21898412", "url": "https://glygen.org/publication/PubMed/21898412" } ] }, { "title": "Inhibition of focal adhesion kinase by PF-562,271 inhibits the growth and metastasis of pancreatic cancer concomitant with altering the tumor microenvironment.", "journal": "Molecular cancer therapeutics", "date": "2011", "authors": "Stokes JB, Adair SJ, Slack-Davis JK, Walters DM, Tilghman RW, Hershey ED, Lowrey B, Thomas KS, Bouton AH, Hwang RF, Stelow EB, Parsons JT, Bauer TW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21903606", "url": "https://glygen.org/publication/PubMed/21903606" } ] }, { "title": "CD147-targeting siRNA inhibits cell-matrix adhesion of human malignant melanoma cells by phosphorylating focal adhesion kinase.", "journal": "The Journal of dermatology", "date": "2012", "authors": "Nishibaba R, Higashi Y, Su J, Furukawa T, Kawai K, Kanekura T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21967109", "url": "https://glygen.org/publication/PubMed/21967109" } ] }, { "title": "The C terminus of talin links integrins to cell cycle progression.", "journal": "The Journal of cell biology", "date": "2011-10-31", "authors": "Wang Pengbo, Ballestrem Christoph, Streuli Charles H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22042621", "url": "https://glygen.org/publication/PubMed/22042621" } ] }, { "title": "Stanniocalcin-1 regulates re-epithelialization in human keratinocytes.", "journal": "PloS one", "date": "2011", "authors": "Yeung BH, Wong CK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22069492", "url": "https://glygen.org/publication/PubMed/22069492" } ] }, { "title": "SOX2-RNAi attenuates S-phase entry and induces RhoA-dependent switch to protease-independent amoeboid migration in human glioma cells.", "journal": "Molecular cancer", "date": "2011", "authors": "Oppel F, Muller N, Schackert G, Hendruschk S, Martin D, Geiger KD, Temme A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22070920", "url": "https://glygen.org/publication/PubMed/22070920" } ] }, { "title": "Tyrosine phosphorylation of cortactin by the FAK-Src complex at focal adhesions regulates cell motility.", "journal": "BMC cell biology", "date": "2011", "authors": "Wang W, Liu Y, Liao K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22078467", "url": "https://glygen.org/publication/PubMed/22078467" } ] }, { "title": "The involvement of integrin beta1 signaling in the migration and myofibroblastic differentiation of skin fibroblasts on anisotropic collagen-containing nanofibers.", "journal": "Biomaterials", "date": "2012", "authors": "Huang C, Fu X, Liu J, Qi Y, Li S, Wang H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22136719", "url": "https://glygen.org/publication/PubMed/22136719" } ] }, { "title": "Enhanced integrin mediated signaling and cell cycle progression on fibronectin mimetic peptide amphiphile monolayers.", "journal": "Langmuir : the ACS journal of surfaces and colloids", "date": "2012-01-24", "authors": "Shroff Kamlesh, Pearce Timothy R, Kokkoli Efrosini", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22149259", "url": "https://glygen.org/publication/PubMed/22149259" } ] }, { "title": "Latent KSHV infection of endothelial cells induces integrin beta3 to activate angiogenic phenotypes.", "journal": "PLoS pathogens", "date": "2011", "authors": "DiMaio TA, Gutierrez KD, Lagunoff M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22174684", "url": "https://glygen.org/publication/PubMed/22174684" } ] }, { "title": "Soluble THSD7A is an N-glycoprotein that promotes endothelial cell migration and tube formation in angiogenesis.", "journal": "PloS one", "date": "2011", "authors": "Kuo MW, Wang CH, Wu HC, Chang SJ, Chuang YJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22194972", "url": "https://glygen.org/publication/PubMed/22194972" } ] }, { "title": "Apc mutation enhances PyMT-induced mammary tumorigenesis.", "journal": "PloS one", "date": "2011", "authors": "Prosperi JR, Khramtsov AI, Khramtsova GF, Goss KH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22216254", "url": "https://glygen.org/publication/PubMed/22216254" } ] }, { "title": "Mda-9/syntenin is expressed in uveal melanoma and correlates with metastatic progression.", "journal": "PloS one", "date": "2012", "authors": "Gangemi R, Mirisola V, Barisione G, Fabbi M, Brizzolara A, Lanza F, Mosci C, Salvi S, Gualco M, Truini M, Angelini G, Boccardo S, Cilli M, Airoldi I, Queirolo P, Jager MJ, Daga A, Pfeffer U, Ferrini S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22267972", "url": "https://glygen.org/publication/PubMed/22267972" } ] }, { "title": "FAK promotes recruitment of talin to nascent adhesions to control cell motility.", "journal": "The Journal of cell biology", "date": "2012-01-23", "authors": "Lawson Christine, Lim Ssang-Taek, Uryu Sean, Chen Xiao Lei, Calderwood David A, Schlaepfer David D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22270917", "url": "https://glygen.org/publication/PubMed/22270917" } ] }, { "title": "MG63 osteoblast-like cells exhibit different behavior when grown on electrospun collagen matrix versus electrospun gelatin matrix.", "journal": "PloS one", "date": "2012", "authors": "Tsai SW, Liou HM, Lin CJ, Kuo KL, Hung YS, Weng RC, Hsu FY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22319618", "url": "https://glygen.org/publication/PubMed/22319618" } ] }, { "title": "ADAM15 protein amplifies focal adhesion kinase phosphorylation under genotoxic stress conditions.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Fried D, Bohm BB, Krause K, Burkhardt H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741" } ] }, { "title": "The Src SH2 domain interacts dynamically with the focal adhesion kinase binding site as demonstrated by paramagnetic NMR spectroscopy.", "journal": "IUBMB life", "date": "2012", "authors": "Lindfors HE, Drijfhout JW, Ubbink M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22550026", "url": "https://glygen.org/publication/PubMed/22550026" } ] }, { "title": "uPAR and cathepsin B knockdown inhibits radiation-induced PKC integrated integrin signaling to the cytoskeleton of glioma-initiating cells.", "journal": "International journal of oncology", "date": "2012", "authors": "Alapati K, Gopinath S, Malla RR, Dasari VR, Rao JS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22641287", "url": "https://glygen.org/publication/PubMed/22641287" } ] }, { "title": "Adhesion-mediated cytoskeletal remodeling is controlled by the direct scaffolding of Src from FAK complexes to lipid rafts by SSeCKS/AKAP12.", "journal": "Oncogene", "date": "2013", "authors": "Su B, Gao L, Meng F, Guo LW, Rothschild J, Gelman IH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22710722", "url": "https://glygen.org/publication/PubMed/22710722" } ] }, { "title": "Nuclear-localized focal adhesion kinase regulates inflammatory VCAM-1 expression.", "journal": "The Journal of cell biology", "date": "2012", "authors": "Lim ST, Miller NL, Chen XL, Tancioni I, Walsh CT, Lawson C, Uryu S, Weis SM, Cheresh DA, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22734001", "url": "https://glygen.org/publication/PubMed/22734001" } ] }, { "title": "Anti-tumor effect of a novel FAK inhibitor TAE226 against human oral squamous cell carcinoma.", "journal": "Oral oncology", "date": "2012", "authors": "Kurio N, Shimo T, Fukazawa T, Okui T, Hassan NM, Honami T, Horikiri Y, Hatakeyama S, Takaoka M, Naomoto Y, Sasaki A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22766511", "url": "https://glygen.org/publication/PubMed/22766511" } ] }, { "title": "GSK3beta inhibition blocks melanoma cell/host interactions by downregulating N-cadherin expression and decreasing FAK phosphorylation.", "journal": "The Journal of investigative dermatology", "date": "2012", "authors": "John JK, Paraiso KH, Rebecca VW, Cantini LP, Abel EV, Pagano N, Meggers E, Mathew R, Krepler C, Izumi V, Fang B, Koomen JM, Messina JL, Herlyn M, Smalley KS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22810307", "url": "https://glygen.org/publication/PubMed/22810307" } ] }, { "title": "Integrin beta5 contributes to the tumorigenic potential of breast cancer cells through the Src-FAK and MEK-ERK signaling pathways.", "journal": "Oncogene", "date": "2013", "authors": "Bianchi-Smiraglia A, Paesante S, Bakin AV", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793" } ] }, { "title": "MicroRNA-7 inhibits epithelial-to-mesenchymal transition and metastasis of breast cancer cells via targeting FAK expression.", "journal": "PloS one", "date": "2012", "authors": "Kong X, Li G, Yuan Y, He Y, Wu X, Zhang W, Wu Z, Chen T, Wu W, Lobie PE, Zhu T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22876288", "url": "https://glygen.org/publication/PubMed/22876288" } ] }, { "title": "Mda-9/syntenin promotes human brain glioma migration through focal adhesion kinase (FAK)-JNK and FAK-AKT signaling.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "date": "2012", "authors": "Zhong D, Ran JH, Tang WY, Zhang XD, Tan Y, Chen GJ, Li XS, Yan Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" } ] }, { "title": "Cortactin as a target for FAK in the regulation of focal adhesion dynamics.", "journal": "PloS one", "date": "2012", "authors": "Tomar A, Lawson C, Ghassemian M, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22952866", "url": "https://glygen.org/publication/PubMed/22952866" } ] }, { "title": "Impaired c-src activation and motility defects in PEA3-null fibroblasts.", "journal": "Biochimica et biophysica acta", "date": "2012-12", "authors": "Chaar Ziad Y, Hastings Laura, Sriram Roshan, McKay Marlene, Antonova Lilia, Hassell John A, Sabourin Luc A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22982417", "url": "https://glygen.org/publication/PubMed/22982417" } ] }, { "title": "Mass production of nanofibrous extracellular matrix with controlled 3D morphology for large-scale soft tissue regeneration.", "journal": "Tissue engineering. Part C, Methods", "date": "2013", "authors": "Alamein MA, Stephens S, Liu Q, Skabo S, Warnke PH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23102268", "url": "https://glygen.org/publication/PubMed/23102268" } ] }, { "title": "Crosstalk between EGFR and integrin affects invasion and proliferation of gastric cancer cell line, SGC7901.", "journal": "OncoTargets and therapy", "date": "2012", "authors": "Dan L, Jian D, Na L, Xiaozhong W", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23109808", "url": "https://glygen.org/publication/PubMed/23109808" } ] }, { "title": "SLK-mediated phosphorylation of paxillin is required for focal adhesion turnover and cell migration.", "journal": "Oncogene", "date": "2013", "authors": "Quizi JL, Baron K, Al-Zahrani KN, O'Reilly P, Sriram RK, Conway J, Laurin AA, Sabourin LA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23128389", "url": "https://glygen.org/publication/PubMed/23128389" } ] }, { "title": "Rap1 can bypass the FAK-Src-Paxillin cascade to induce cell spreading and focal adhesion formation.", "journal": "PloS one", "date": "2012", "authors": "Ross SH, Spanjaard E, Post A, Vliem MJ, Kristyanto H, Bos JL, de Rooij J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" } ] }, { "title": "Akt1 promotes focal adhesion disassembly and cell motility through phosphorylation of FAK in growth factor-stimulated cells.", "journal": "Journal of cell science", "date": "2013", "authors": "Higuchi M, Kihara R, Okazaki T, Aoki I, Suetsugu S, Gotoh Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ] }, { "title": "Inhibiting the interaction of cMET and IGF-1R with FAK effectively reduces growth of pancreatic cancer cells in vitro and in vivo.", "journal": "Anti-cancer agents in medicinal chemistry", "date": "2013", "authors": "Ucar DA, Magis AT, He DH, Lawrence NJ, Sebti SM, Kurenova E, Zajac-Kaye M, Zhang J, Hochwald SN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23272972", "url": "https://glygen.org/publication/PubMed/23272972" } ] }, { "title": "Targeting constitutively activated beta1 integrins inhibits prostate cancer metastasis.", "journal": "Molecular cancer research : MCR", "date": "2013", "authors": "Lee YC, Jin JK, Cheng CJ, Huang CF, Song JH, Huang M, Brown WS, Zhang S, Yu-Lee LY, Yeh ET, McIntyre BW, Logothetis CJ, Gallick GE, Lin SH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23339185", "url": "https://glygen.org/publication/PubMed/23339185" } ] }, { "title": "The tumor suppressor gene ARHI (DIRAS3) inhibits ovarian cancer cell migration through multiple mechanisms.", "journal": "Cell adhesion & migration", "date": "2013", "authors": "Lu Z, Bast RC Jr", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23357870", "url": "https://glygen.org/publication/PubMed/23357870" } ] }, { "title": "Progesterone receptor isoforms PRA and PRB differentially contribute to breast cancer cell migration through interaction with focal adhesion kinase complexes.", "journal": "Molecular biology of the cell", "date": "2013", "authors": "Bellance C, Khan JA, Meduri G, Guiochon-Mantel A, Lombes M, Loosfelt H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23485561", "url": "https://glygen.org/publication/PubMed/23485561" } ] }, { "title": "cAMP Elevation Down-Regulates beta3 Integrin and Focal Adhesion Kinase and Inhibits Leptin-Induced Migration of MDA-MB-231 Breast Cancer Cells.", "journal": "BioResearch open access", "date": "2012", "authors": "Spina A, Di Maiolo F, Esposito A, Sapio L, Chiosi E, Sorvillo L, Naviglio S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23515360", "url": "https://glygen.org/publication/PubMed/23515360" } ] }, { "title": "Prostaglandin E\u2082 receptor EP1-mediated phosphorylation of focal adhesion kinase enhances cell adhesion and migration in hepatocellular carcinoma cells.", "journal": "International journal of oncology", "date": "2013-05", "authors": "Bai Xiaoming, Wang Jie, Zhang Li, Ma Juan, Zhang Hai, Xia Shukai, Zhang Min, Ma Xiuping, Guo Yan, Rong Rong, Cheng Shanyu, Shu Wei, Wang Yipin, Leng Jing", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23525457", "url": "https://glygen.org/publication/PubMed/23525457" } ] }, { "title": "ERBB4 confers metastatic capacity in Ewing sarcoma.", "journal": "EMBO molecular medicine", "date": "2013", "authors": "Mendoza-Naranjo A, El-Naggar A, Wai DH, Mistry P, Lazic N, Ayala FR, da Cunha IW, Rodriguez-Viciana P, Cheng H, Tavares Guerreiro Fregnani JH, Reynolds P, Arceci RJ, Nicholson A, Triche TJ, Soares FA, Flanagan AM, Wang YZ, Strauss SJ, Sorensen PH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23681745", "url": "https://glygen.org/publication/PubMed/23681745" } ] }, { "title": "Prolactin-induced protein (PIP) regulates proliferation of luminal A type breast cancer cells in an estrogen-independent manner.", "journal": "PloS one", "date": "2014", "authors": "Baniwal SK, Chimge NO, Jordan VC, Tripathy D, Frenkel B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23755096", "url": "https://glygen.org/publication/PubMed/23755096" } ] }, { "title": "\u03b1\u03bd and \u03b21 Integrins mediate A\u03b2-induced neurotoxicity in hippocampal neurons via the FAK signaling pathway.", "journal": "PloS one", "date": "2014", "authors": "Han Hai-Yan, Zhang Jin-Ping, Ji Su-Qiong, Liang Qi-Ming, Kang Hui-Cong, Tang Rong-Hua, Zhu Sui-Qiang, Xue Zheng", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23755149", "url": "https://glygen.org/publication/PubMed/23755149" } ] }, { "title": "Focal adhesion kinase autophosphorylation inhibition decreases colon cancer cell growth and enhances the efficacy of chemotherapy.", "journal": "Cancer biology & therapy", "date": "2013", "authors": "Heffler M, Golubovskaya VM, Dunn KM, Cance W", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23792569", "url": "https://glygen.org/publication/PubMed/23792569" } ] }, { "title": "KLF8 and FAK cooperatively enrich the active MMP14 on the cell surface required for the metastatic progression of breast cancer.", "journal": "Oncogene", "date": "2014", "authors": "Lu H, Hu L, Yu L, Wang X, Urvalek AM, Li T, Shen C, Mukherjee D, Lahiri SK, Wason MS, Zhao J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23812425", "url": "https://glygen.org/publication/PubMed/23812425" } ] }, { "title": "Mechanically activated Fyn utilizes mTORC2 to regulate RhoA and adipogenesis in mesenchymal stem cells.", "journal": "Stem cells (Dayton, Ohio)", "date": "2013", "authors": "Thompson WR, Guilluy C, Xie Z, Sen B, Brobst KE, Yen SS, Uzer G, Styner M, Case N, Burridge K, Rubin J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23836527", "url": "https://glygen.org/publication/PubMed/23836527" } ] }, { "title": "[Role of focal adhesion kinase in adhesion and migration of Hep G2 cells].", "journal": "Sheng wu yi xue gong cheng xue za zhi = Journal of biomedical engineering = Shengwu yixue gongchengxue zazhi", "date": "2013", "authors": "Ma Y, Shen Y, Ren H, Sun H, Yu H, Lin X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23858760", "url": "https://glygen.org/publication/PubMed/23858760" } ] }, { "title": "Ouabain suppresses the migratory behavior of lung cancer cells.", "journal": "PloS one", "date": "2013", "authors": "Pongrakhananon V, Chunhacha P, Chanvorachote P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23874694", "url": "https://glygen.org/publication/PubMed/23874694" } ] }, { "title": "Curcumin Suppresses Metastasis via Sp-1, FAK Inhibition, and E-Cadherin Upregulation in Colorectal Cancer.", "journal": "Evidence-based complementary and alternative medicine : eCAM", "date": "2013", "authors": "Chen CC, Sureshbabul M, Chen HW, Lin YS, Lee JY, Hong QS, Yang YC, Yu SL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" } ] }, { "title": "Long-term nitric oxide exposure enhances lung cancer cell migration.", "journal": "BioMed research international", "date": "2013", "authors": "Sanuphan Arpasinee, Chunhacha Preedakorn, Pongrakhananon Varisa, Chanvorachote Pithi", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23984323", "url": "https://glygen.org/publication/PubMed/23984323" } ] }, { "title": "Costamere remodeling with muscle loading and unloading in healthy young men.", "journal": "Journal of anatomy", "date": "2013", "authors": "Li R, Narici MV, Erskine RM, Seynnes OR, Rittweger J, Pisot R, Simunic B, Fluck M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24010829", "url": "https://glygen.org/publication/PubMed/24010829" } ] }, { "title": "Optimising parameters for the differentiation of SH-SY5Y cells to study cell adhesion and cell migration.", "journal": "BMC research notes", "date": "2013-09-11", "authors": "Dwane Susan, Durack Edel, Kiely Patrick A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24025096", "url": "https://glygen.org/publication/PubMed/24025096" } ] }, { "title": "Integrin - dependent mechanotransduction in mechanically stimulated human annulus fibrosus cells: evidence for an alternative mechanotransduction pathway operating with degeneration.", "journal": "PloS one", "date": "2013", "authors": "Gilbert HT, Nagra NS, Freemont AJ, Millward-Sadler SJ, Hoyland JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24039840", "url": "https://glygen.org/publication/PubMed/24039840" } ] }, { "title": "Estradiol and tamoxifen induce cell migration through GPR30 and activation of focal adhesion kinase (FAK) in endometrial cancers with low or without nuclear estrogen receptor alpha (ERalpha).", "journal": "PloS one", "date": "2013", "authors": "Tsai CL, Wu HM, Lin CY, Lin YJ, Chao A, Wang TH, Hsueh S, Lai CH, Wang HS", "evidence": [ { "database": "Reactome", "id": "R-HSA-9634638", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-9634638" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24039841", "url": "https://glygen.org/publication/PubMed/24039841" } ] }, { "title": "Integrin-specific control of focal adhesion kinase and RhoA regulates membrane protrusion and invasion.", "journal": "PloS one", "date": "2013", "authors": "Costa P, Scales TM, Ivaska J, Parsons M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24040310", "url": "https://glygen.org/publication/PubMed/24040310" } ] }, { "title": "The overexpression of scaffolding protein NEDD9 promotes migration and invasion in cervical cancer via tyrosine phosphorylated FAK and SRC.", "journal": "PloS one", "date": "2013", "authors": "Sima Ni, Cheng Xiaodong, Ye Feng, Ma Ding, Xie Xing, L\u00fc Weiguo", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24058594", "url": "https://glygen.org/publication/PubMed/24058594" } ] }, { "title": "Role of focal adhesion kinase in regulating YB-1-mediated paclitaxel resistance in ovarian cancer.", "journal": "Journal of the National Cancer Institute", "date": "2013", "authors": "Kang Y, Hu W, Ivan C, Dalton HJ, Miyake T, Pecot CV, Zand B, Liu T, Huang J, Jennings NB, Rupaimoole R, Taylor M, Pradeep S, Wu SY, Lu C, Wen Y, Huang J, Liu J, Sood AK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24062525", "url": "https://glygen.org/publication/PubMed/24062525" } ] }, { "title": "Role of material-driven fibronectin fibrillogenesis in protein remodeling.", "journal": "BioResearch open access", "date": "2013-10", "authors": "Llopis-Hern\u00e1ndez Virginia, Rico Patricia, Moratal David, Altankov George, Salmer\u00f3n-S\u00e1nchez Manuel", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24083092", "url": "https://glygen.org/publication/PubMed/24083092" } ] }, { "title": "EGFR/MEK/ERK/CDK5-dependent integrin-independent FAK phosphorylated on serine 732 contributes to microtubule depolymerization and mitosis in tumor cells.", "journal": "Cell death & disease", "date": "2013-10-03", "authors": "Rea K, Sensi M, Anichini A, Canevari S, Tomassetti A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658" } ] }, { "title": "CDK5 is essential for TGF-beta1-induced epithelial-mesenchymal transition and breast cancer progression.", "journal": "Scientific reports", "date": "2013", "authors": "Liang Q, Li L, Zhang J, Lei Y, Wang L, Liu DX, Feng J, Hou P, Yao R, Zhang Y, Huang B, Lu J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24121667", "url": "https://glygen.org/publication/PubMed/24121667" } ] }, { "title": "Osteoblast adhesion dynamics: a possible role for ROS and LMW-PTP.", "journal": "Journal of cellular biochemistry", "date": "2014", "authors": "Fernandes GV, Cavagis AD, Ferreira CV, Olej B, Leao Mde S, Yano CL, Peppelenbosch M, Granjeiro JM, Zambuzzi WF", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24123071", "url": "https://glygen.org/publication/PubMed/24123071" } ] }, { "title": "Phosphoproteomic profiling identifies focal adhesion kinase as a mediator of docetaxel resistance in castrate-resistant prostate cancer.", "journal": "Molecular cancer therapeutics", "date": "2014", "authors": "Lee BY, Hochgrafe F, Lin HM, Castillo L, Wu J, Raftery MJ, Martin Shreeve S, Horvath LG, Daly RJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24194567", "url": "https://glygen.org/publication/PubMed/24194567" } ] }, { "title": "Pancreatic stellate cells promote hapto-migration of cancer cells through collagen I-mediated signalling pathway.", "journal": "British journal of cancer", "date": "2014", "authors": "Lu J, Zhou S, Siech M, Habisch H, Seufferlein T, Bachem MG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24201748", "url": "https://glygen.org/publication/PubMed/24201748" } ] }, { "title": "Requirement of PEA3 for transcriptional activation of FAK gene in tumor metastasis.", "journal": "PloS one", "date": "2013", "authors": "Li Shufeng, Huang Xiaofeng, Zhang Dapeng, Huang Qilai, Pei Guoshun, Wang Lixiang, Jiang Wenhui, Hu Qingang, Tan Renxiang, Hua Zi-Chun", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24260201", "url": "https://glygen.org/publication/PubMed/24260201" } ] }, { "title": "Integrin-matrix clusters form podosome-like adhesions in the absence of traction forces.", "journal": "Cell reports", "date": "2013-12-12", "authors": "Yu Cheng-han, Rafiq Nisha Bte Mohd, Krishnasamy Anitha, Hartman Kevin L, Jones Gareth E, Bershadsky Alexander D, Sheetz Michael P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24290759", "url": "https://glygen.org/publication/PubMed/24290759" } ] }, { "title": "Angiopoietin-like 3 induces podocyte F-actin rearrangement through integrin alpha(V)beta(3)/FAK/PI3K pathway-mediated Rac1 activation.", "journal": "BioMed research international", "date": "2013", "authors": "Lin Y, Rao J, Zha XL, Xu H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24294595", "url": "https://glygen.org/publication/PubMed/24294595" } ] }, { "title": "Somatic mutational analysis of FAK in breast cancer: a novel gain-of-function mutation due to deletion of exon 33.", "journal": "Biochemical and biophysical research communications", "date": "2014-01-10", "authors": "Fang Xu-Qian, Liu Xiang-Fan, Yao Ling, Chen Chang-Qiang, Gu Zhi-Dong, Ni Pei-Hua, Zheng Xin-Min, Fan Qi-Shi", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24360952", "url": "https://glygen.org/publication/PubMed/24360952" } ] }, { "title": "Dysregulation of microRNA-34a expression in colorectal cancer inhibits the phosphorylation of FAK via VEGF.", "journal": "Digestive diseases and sciences", "date": "2014-05", "authors": "Zhang Danhua, Zhou Jianping, Dong Ming", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24370784", "url": "https://glygen.org/publication/PubMed/24370784" } ] }, { "title": "Focal adhesion kinase is a regulator of F-actin dynamics: New insights from studies in the testis.", "journal": "Spermatogenesis", "date": "2013", "authors": "Li SY, Mruk DD, Cheng CY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24381802", "url": "https://glygen.org/publication/PubMed/24381802" } ] }, { "title": "CD13 promotes mesenchymal stem cell-mediated regeneration of ischemic muscle.", "journal": "Frontiers in physiology", "date": "2014", "authors": "Rahman MM, Subramani J, Ghosh M, Denninger JK, Takeda K, Fong GH, Carlson ME, Shapiro LH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24409152", "url": "https://glygen.org/publication/PubMed/24409152" } ] }, { "title": "Down-regulation of Gli transcription factor leads to the inhibition of migration and invasion of ovarian cancer cells via integrin beta4-mediated FAK signaling.", "journal": "PloS one", "date": "2014", "authors": "Chen Q, Xu R, Zeng C, Lu Q, Huang D, Shi C, Zhang W, Deng L, Yan R, Rao H, Gao G, Luo S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24533083", "url": "https://glygen.org/publication/PubMed/24533083" } ] }, { "title": "The 2-pore domain potassium channel TREK-1 regulates stretch-induced detachment of alveolar epithelial cells.", "journal": "PloS one", "date": "2014", "authors": "Roan E, Waters CM, Teng B, Ghosh M, Schwingshackl A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24586773", "url": "https://glygen.org/publication/PubMed/24586773" } ] }, { "title": "A photoactivatable nanopatterned substrate for analyzing collective cell migration with precisely tuned cell-extracellular matrix ligand interactions.", "journal": "PloS one", "date": "2014", "authors": "Shimizu Yoshihisa, Boehm Heike, Yamaguchi Kazuo, Spatz Joachim P, Nakanishi Jun", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24632806", "url": "https://glygen.org/publication/PubMed/24632806" } ] }, { "title": "Altering FAK-paxillin interactions reduces adhesion, migration and invasion processes.", "journal": "PloS one", "date": "2014", "authors": "Deramaudt Th\u00e9r\u00e8se B, Dujardin Denis, Noulet Fanny, Martin Sophie, Vauchelles Romain, Takeda Ken, Rond\u00e9 Philippe", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" } ] }, { "title": "Ambivalent role of pFAK-Y397 in serous ovarian cancer--a study of the OVCAD consortium.", "journal": "Molecular cancer", "date": "2014", "authors": "Aust S, Auer K, Bachmayr-Heyda A, Denkert C, Sehouli J, Braicu I, Mahner S, Lambrechts S, Vergote I, Grimm C, Horvat R, Castillo-Tong DC, Zeillinger R, Pils D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24655477", "url": "https://glygen.org/publication/PubMed/24655477" } ] }, { "title": "Biglycan enhances gastric cancer invasion by activating FAK signaling pathway.", "journal": "Oncotarget", "date": "2014", "authors": "Hu L, Duan YT, Li JF, Su LP, Yan M, Zhu ZG, Liu BY, Yang QM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" } ] }, { "title": "A site-specific phosphorylation of the focal adhesion kinase controls the formation of spheroid cell clusters.", "journal": "Neurochemical research", "date": "2014", "authors": "Beck HC, Gosau M, Kristensen LP, Morsczeck C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24706070", "url": "https://glygen.org/publication/PubMed/24706070" } ] }, { "title": "The marine-derived sipholenol A-4-O-3',4'-dichlorobenzoate inhibits breast cancer growth and motility in vitro and in vivo through the suppression of Brk and FAK signaling.", "journal": "Marine drugs", "date": "2014", "authors": "Akl MR, Foudah AI, Ebrahim HY, Meyer SA, El Sayed KA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" } ] }, { "title": "Focal adhesion kinase regulates the activity of the osmosensitive transcription factor TonEBP/NFAT5 under hypertonic conditions.", "journal": "Frontiers in physiology", "date": "2014", "authors": "Neuhofer W, Kuper C, Lichtnekert J, Holzapfel K, Rupanagudi KV, Fraek ML, Bartels H, Beck FX", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24772088", "url": "https://glygen.org/publication/PubMed/24772088" } ] }, { "title": "Analyses of merlin/NF2 connection to FAK inhibitor responsiveness in serous ovarian cancer.", "journal": "Gynecologic oncology", "date": "2014", "authors": "Shah NR, Tancioni I, Ward KK, Lawson C, Chen XL, Jean C, Sulzmaier FJ, Uryu S, Miller NL, Connolly DC, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24786638", "url": "https://glygen.org/publication/PubMed/24786638" } ] }, { "title": "Vimentin regulates lung cancer cell adhesion through a VAV2-Rac1 pathway to control focal adhesion kinase activity.", "journal": "Oncogene", "date": "2015", "authors": "Havel LS, Kline ER, Salgueiro AM, Marcus AI", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24858039", "url": "https://glygen.org/publication/PubMed/24858039" } ] }, { "title": "Essential function for PDLIM2 in cell polarization in three-dimensional cultures by feedback regulation of the beta1-integrin-RhoA signaling axis.", "journal": "Neoplasia (New York, N.Y.)", "date": "2014", "authors": "Deevi RK, Cox OT, O'Connor R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24863845", "url": "https://glygen.org/publication/PubMed/24863845" } ] }, { "title": "An aberrant spliced transcript of focal adhesion kinase is exclusively expressed in human breast cancer.", "journal": "Journal of translational medicine", "date": "2014", "authors": "Yao L, Li K, Peng W, Lin Q, Li S, Hu X, Zheng X, Shao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534" } ] }, { "title": "Maternal embryonic leucine zipper kinase enhances gastric cancer progression via the FAK/Paxillin pathway.", "journal": "Molecular cancer", "date": "2014", "authors": "Du T, Qu Y, Li J, Li H, Su L, Zhou Q, Yan M, Li C, Zhu Z, Liu B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" } ] }, { "title": "Alpha-mangostin inhibits intracellular fatty acid synthase and induces apoptosis in breast cancer cells.", "journal": "Molecular cancer", "date": "2014", "authors": "Li P, Tian W, Ma X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24894151", "url": "https://glygen.org/publication/PubMed/24894151" } ] }, { "title": "Redox modulation of FAK controls melanoma survival--role of NOX4.", "journal": "PloS one", "date": "2014", "authors": "Ribeiro-Pereira C, Moraes JA, Souza Mde J, Laurindo FR, Arruda MA, Barja-Fidalgo C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24911159", "url": "https://glygen.org/publication/PubMed/24911159" } ] }, { "title": "Nanometer scale titanium surface texturing are detected by signaling pathways involving transient FAK and Src activations.", "journal": "PloS one", "date": "2014", "authors": "Zambuzzi Willian F, Bonfante Estevam A, Jimbo Ryo, Hayashi Mariko, Andersson Martin, Alves Gutemberg, Takamori Esther R, Beltr\u00e3o Paulo J, Coelho Paulo G, Granjeiro Jos\u00e9 M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24999733", "url": "https://glygen.org/publication/PubMed/24999733" } ] }, { "title": "Inhibition of smooth muscle force generation by focal adhesion kinase inhibitors in the hyperplastic human prostate.", "journal": "American journal of physiology. Renal physiology", "date": "2014", "authors": "Kunit T, Gratzke C, Schreiber A, Strittmatter F, Waidelich R, Rutz B, Loidl W, Andersson KE, Stief CG, Hennenberg M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25056351", "url": "https://glygen.org/publication/PubMed/25056351" } ] }, { "title": "Focal adhesion kinase inhibitors in the treatment of metastatic cancer: a patent review.", "journal": "Expert opinion on therapeutic patents", "date": "2014", "authors": "Shanthi E, Krishna MH, Arunesh GM, Venkateswara Reddy K, Sooriya Kumar J, Viswanadhan VN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25113248", "url": "https://glygen.org/publication/PubMed/25113248" } ] }, { "title": "CCN1 induces oncostatin M production in osteoblasts via integrin-dependent signal pathways.", "journal": "PloS one", "date": "2014", "authors": "Chen CY, Su CM, Huang YL, Tsai CH, Fuh LJ, Tang CH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25187949", "url": "https://glygen.org/publication/PubMed/25187949" } ] }, { "title": "Overcoming EMT-associated resistance to anti-cancer drugs via Src/FAK pathway inhibition.", "journal": "Oncotarget", "date": "2014", "authors": "Wilson C, Nicholes K, Bustos D, Lin E, Song Q, Stephan JP, Kirkpatrick DS, Settleman J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" } ] }, { "title": "New insights into FAK phosphorylation based on a FAT domain-defective mutation.", "journal": "PloS one", "date": "2014", "authors": "Fang X, Liu X, Yao L, Chen C, Lin J, Ni P, Zheng X, Fan Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25226367", "url": "https://glygen.org/publication/PubMed/25226367" } ] }, { "title": "FAK inhibition with small molecule inhibitor Y15 decreases viability, clonogenicity, and cell attachment in thyroid cancer cell lines and synergizes with targeted therapeutics.", "journal": "Oncotarget", "date": "2014", "authors": "O'Brien S, Golubovskaya VM, Conroy J, Liu S, Wang D, Liu B, Cance WG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25277206", "url": "https://glygen.org/publication/PubMed/25277206" } ] }, { "title": "beta Integrins mediate FAK Y397 autophosphorylation of resistance arteries during eutrophic inward remodeling in hypertension.", "journal": "Journal of vascular research", "date": "2014", "authors": "Heerkens EH, Quinn L, Withers SB, Heagerty AM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25300309", "url": "https://glygen.org/publication/PubMed/25300309" } ] }, { "title": "Early changes in costameric and mitochondrial protein expression with unloading are muscle specific.", "journal": "BioMed research international", "date": "2014", "authors": "Fluck M, Li R, Valdivieso P, Linnehan RM, Castells J, Tesch P, Gustafsson T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25313365", "url": "https://glygen.org/publication/PubMed/25313365" } ] }, { "title": "A novel synthetic small molecule YH-306 suppresses colorectal tumour growth and metastasis via FAK pathway.", "journal": "Journal of cellular and molecular medicine", "date": "2015", "authors": "Dai F, Chen Y, Huang L, Wang J, Zhang T, Li J, Tong W, Liu M, Yi Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25351103", "url": "https://glygen.org/publication/PubMed/25351103" } ] }, { "title": "CD147 promotes Src-dependent activation of Rac1 signaling through STAT3/DOCK8 during the motility of hepatocellular carcinoma cells.", "journal": "Oncotarget", "date": "2015", "authors": "Wang SJ, Cui HY, Liu YM, Zhao P, Zhang Y, Fu ZG, Chen ZN, Jiang JL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25428919", "url": "https://glygen.org/publication/PubMed/25428919" } ] }, { "title": "A small molecule FAK kinase inhibitor, GSK2256098, inhibits growth and survival of pancreatic ductal adenocarcinoma cells.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2014", "authors": "Zhang J, He DH, Zajac-Kaye M, Hochwald SN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25486573", "url": "https://glygen.org/publication/PubMed/25486573" } ] }, { "title": "Fangchinoline as a kinase inhibitor targets FAK and suppresses FAK-mediated signaling pathway in A549.", "journal": "Journal of drug targeting", "date": "2015", "authors": "Guo B, Su J, Zhang T, Wang K, Li X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25539072", "url": "https://glygen.org/publication/PubMed/25539072" } ] }, { "title": "Loss of anchorage primarily induces non-apoptotic cell death in a human mammary epithelial cell line under atypical focal adhesion kinase signaling.", "journal": "Cell death & disease", "date": "2015-01-22", "authors": "Ishikawa F, Ushida K, Mori K, Shibanuma M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393" } ] }, { "title": "Mertk deficiency affects macrophage directional migration via disruption of cytoskeletal organization.", "journal": "PloS one", "date": "2015", "authors": "Tang Y, Wu S, Liu Q, Xie J, Zhang J, Han D, Lu Q, Lu Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25617898", "url": "https://glygen.org/publication/PubMed/25617898" } ] }, { "title": "Myoferlin depletion elevates focal adhesion kinase and paxillin phosphorylation and enhances cell-matrix adhesion in breast cancer cells.", "journal": "American journal of physiology. Cell physiology", "date": "2015", "authors": "Blackstone BN, Li R, Ackerman WE 4th, Ghadiali SN, Powell HM, Kniss DA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25631868", "url": "https://glygen.org/publication/PubMed/25631868" } ] }, { "title": "Lipopolysaccharide-promoted proliferation of Caco-2 cells is mediated by c-Src induction and ERK activation.", "journal": "BioMedicine", "date": "2015", "authors": "Lin TY, Fan CW, Maa MC, Leu TH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25705585", "url": "https://glygen.org/publication/PubMed/25705585" } ] }, { "title": "OGD induced modification of FAK- and PYK2-coupled pathways in organotypic hippocampal slice cultures.", "journal": "Brain research", "date": "2015", "authors": "Ziemka-Nalecz M, Jaworska J, Sypecka J, Zalewska T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25708150", "url": "https://glygen.org/publication/PubMed/25708150" } ] }, { "title": "FAK activation is required for IGF1R-mediated regulation of EMT, migration, and invasion in mesenchymal triple negative breast cancer cells.", "journal": "Oncotarget", "date": "2015-03-10", "authors": "Taliaferro-Smith LaTonia, Oberlick Elaine, Liu Tongrui, McGlothen Tanisha, Alcaide Tiffanie, Tobin Rachel, Donnelly Siobhan, Commander Rachel, Kline Erik, Nagaraju Ganji Purnachandra, Havel Lauren, Marcus Adam, Nahta Rita, O'Regan Ruth", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25749031", "url": "https://glygen.org/publication/PubMed/25749031" } ] }, { "title": "N-Cadherin Induction by ECM Stiffness and FAK Overrides the Spreading Requirement for Proliferation of Vascular Smooth Muscle Cells.", "journal": "Cell reports", "date": "2015", "authors": "Mui KL, Bae YH, Gao L, Liu SL, Xu T, Radice GL, Chen CS, Assoian RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414" } ] }, { "title": "Ruthenium polypyridyl complex inhibits growth and metastasis of breast cancer cells by suppressing FAK signaling with enhancement of TRAIL-induced apoptosis.", "journal": "Scientific reports", "date": "2015", "authors": "Cao W, Zheng W, Chen T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" } ] }, { "title": "Yes-mediated phosphorylation of focal adhesion kinase at tyrosine 861 increases metastatic potential of prostate cancer cells.", "journal": "Oncotarget", "date": "2015", "authors": "Chatterji T, Varkaris AS, Parikh NU, Song JH, Cheng CJ, Schweppe RE, Alexander S, Davis JW, Troncoso P, Friedl P, Kuang J, Lin SH, Gallick GE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25868388", "url": "https://glygen.org/publication/PubMed/25868388" } ] }, { "title": "FAK activity protects nucleostemin in facilitating breast cancer spheroid and tumor growth.", "journal": "Breast cancer research : BCR", "date": "2015", "authors": "Tancioni I, Miller NL, Uryu S, Lawson C, Jean C, Chen XL, Kleinschmidt EG, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25880415", "url": "https://glygen.org/publication/PubMed/25880415" } ] }, { "title": "Involvement of ROS-alpha v beta 3 integrin-FAK/Pyk2 in the inhibitory effect of melatonin on U251 glioma cell migration and invasion under hypoxia.", "journal": "Journal of translational medicine", "date": "2015", "authors": "Xu CS, Wang ZF, Huang XD, Dai LM, Cao CJ, Li ZQ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25889845", "url": "https://glygen.org/publication/PubMed/25889845" } ] }, { "title": "Biomimetic LBL structured nanofibrous matrices assembled by chitosan/collagen for promoting wound healing.", "journal": "Biomaterials", "date": "2015", "authors": "Huang R, Li W, Lv X, Lei Z, Bian Y, Deng H, Wang H, Li J, Li X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25890707", "url": "https://glygen.org/publication/PubMed/25890707" } ] }, { "title": "Regulation of the microtubular cytoskeleton by Polycystin-1 favors focal adhesions turnover to modulate cell adhesion and migration.", "journal": "BMC cell biology", "date": "2015", "authors": "Castelli M, De Pascalis C, Distefano G, Ducano N, Oldani A, Lanzetti L, Boletta A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25947155", "url": "https://glygen.org/publication/PubMed/25947155" } ] }, { "title": "Pinocembrin suppresses TGF-\u03b21-induced epithelial-mesenchymal transition and metastasis of human Y-79 retinoblastoma cells through inactivating \u03b1v\u03b23 integrin/FAK/p38\u03b1 signaling pathway.", "journal": "Cell & bioscience", "date": "2014", "authors": "Chen Kun-Shiang, Shi Ming-Der, Chien Chi-Sheng, Shih Yuan-Wei", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790" } ] }, { "title": "The role of c-Src in the invasion and metastasis of hepatocellular carcinoma cells induced by association of cell surface GRP78 with activated alpha2M.", "journal": "BMC cancer", "date": "2015", "authors": "Zhao S, Li H, Wang Q, Su C, Wang G, Song H, Zhao L, Luan Z, Su R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25958313", "url": "https://glygen.org/publication/PubMed/25958313" } ] }, { "title": "Corosolic Acid Inhibits Hepatocellular Carcinoma Cell Migration by Targeting the VEGFR2/Src/FAK Pathway.", "journal": "PloS one", "date": "2015", "authors": "Ku CY, Wang YR, Lin HY, Lu SC, Lin JY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25978354", "url": "https://glygen.org/publication/PubMed/25978354" } ] }, { "title": "Cyr61 as mediator of Src signaling in triple negative breast cancer cells.", "journal": "Oncotarget", "date": "2015", "authors": "Sanchez-Bailon MP, Calcabrini A, Mayoral-Varo V, Molinari A, Wagner KU, Losada JP, Ciordia S, Albar JP, Martin-Perez J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25980494", "url": "https://glygen.org/publication/PubMed/25980494" } ] }, { "title": "Doxycycline inhibits leukemic cell migration via inhibition of matrix metalloproteinases and phosphorylation of focal adhesion kinase.", "journal": "Molecular medicine reports", "date": "2015", "authors": "Wang C, Xiang R, Zhang X, Chen Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26004127", "url": "https://glygen.org/publication/PubMed/26004127" } ] }, { "title": "Modulation of focal adhesion constituents and their down-stream events by EGF: On the cross-talk of integrins and growth factor receptors.", "journal": "Biochimica et biophysica acta", "date": "2015", "authors": "Eberwein P, Laird D, Schulz S, Reinhard T, Steinberg T, Tomakidi P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26079101", "url": "https://glygen.org/publication/PubMed/26079101" } ] }, { "title": "TRPM4 Is a Novel Component of the Adhesome Required for Focal Adhesion Disassembly, Migration and Contractility.", "journal": "PloS one", "date": "2015", "authors": "Caceres M, Ortiz L, Recabarren T, Romero A, Colombo A, Leiva-Salcedo E, Varela D, Rivas J, Silva I, Morales D, Campusano C, Almarza O, Simon F, Toledo H, Park KS, Trimmer JS, Cerda O", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26110647", "url": "https://glygen.org/publication/PubMed/26110647" } ] }, { "title": "Focal adhesion kinase-promoted tumor glucose metabolism is associated with a shift of mitochondrial respiration to glycolysis.", "journal": "Oncogene", "date": "2016", "authors": "Zhang J, Gao Q, Zhou Y, Dier U, Hempel N, Hochwald SN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26119934", "url": "https://glygen.org/publication/PubMed/26119934" } ] }, { "title": "CD99 inhibits CD98-mediated beta1 integrin signaling through SHP2-mediated FAK dephosphorylation.", "journal": "Experimental cell research", "date": "2015", "authors": "Lee KJ, Yoo YH, Kim MS, Yadav BK, Kim Y, Lim D, Hwangbo C, Moon KW, Kim D, Jeoung D, Lee H, Lee JH, Hahn JH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26172215", "url": "https://glygen.org/publication/PubMed/26172215" } ] }, { "title": "Adhesion to fibronectin regulates Hippo signaling via the FAK-Src-PI3K pathway.", "journal": "The Journal of cell biology", "date": "2015-08-03", "authors": "Kim Nam-Gyun, Gumbiner Barry M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26216901", "url": "https://glygen.org/publication/PubMed/26216901" } ] }, { "title": "Differential Expression of Adhesion-Related Proteins and MAPK Pathways Lead to Suitable Osteoblast Differentiation of Human Mesenchymal Stem Cells Subpopulations.", "journal": "Stem cells and development", "date": "2015-11-01", "authors": "Leyva-Leyva Margarita, L\u00f3pez-D\u00edaz Annia, Barrera Lourdes, Camacho-Morales Alberto, Hernandez-Aguilar Felipe, Carrillo-Casas Erika M, Arriaga-Pizano Lourdes, Calder\u00f3n-P\u00e9rez Jaime, Garc\u00eda-\u00c1lvarez Jorge, Orozco-Hoyuela Gabriel, Pi\u00f1a-Barba Cristina, Rojas-Mart\u00ednez Augusto, Romero-D\u00edaz V\u00edktor, Lara-Arias Jorge, Rivera-Bola\u00f1os Nancy, L\u00f3pez-Camarillo C\u00e9sar, Moncada-Saucedo Nidia, Galv\u00e1n-De los Santos Alejandra, Meza-Urz\u00faa F\u00e1tima, Villarreal-G\u00f3mez Luis, Fuentes-Mera Lizeth", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26230358", "url": "https://glygen.org/publication/PubMed/26230358" } ] }, { "title": "UBE2S is associated with malignant characteristics of breast cancer cells.", "journal": "Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine", "date": "2016", "authors": "Ayesha AK, Hyodo T, Asano E, Sato N, Mansour MA, Ito S, Hamaguchi M, Senga T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26245992", "url": "https://glygen.org/publication/PubMed/26245992" } ] }, { "title": "Divergent modulation of Rho-kinase and Ca(2+) influx pathways by Src family kinases and focal adhesion kinase in airway smooth muscle.", "journal": "British journal of pharmacology", "date": "2015", "authors": "Shaifta Y, Irechukwu N, Prieto-Lloret J, MacKay CE, Marchon KA, Ward JP, Knock GA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26294392", "url": "https://glygen.org/publication/PubMed/26294392" } ] }, { "title": "Cytoglobin expression in the hepatic stellate cell line HSC-T6 is regulated by extracellular matrix proteins dependent on FAK-signalling.", "journal": "Fibrogenesis & tissue repair", "date": "2015", "authors": "Stone LC, Thorne LS, Weston CJ, Graham M, Hodges NJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26300973", "url": "https://glygen.org/publication/PubMed/26300973" } ] }, { "title": "LRRK2 G2019S mutation attenuates microglial motility by inhibiting focal adhesion kinase.", "journal": "Nature communications", "date": "2015", "authors": "Choi I, Kim B, Byun JW, Baik SH, Huh YH, Kim JH, Mook-Jung I, Song WK, Shin JH, Seo H, Suh YH, Jou I, Park SM, Kang HC, Joe EH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26365310", "url": "https://glygen.org/publication/PubMed/26365310" } ] }, { "title": "Automated tracking of tumor-stroma morphology in microtissues identifies functional targets within the tumor microenvironment for therapeutic intervention.", "journal": "Oncotarget", "date": "2015-10-06", "authors": "\u00c5kerfelt Malin, Bayramoglu Neslihan, Robinson Sean, Toriseva Mervi, Schukov Hannu-Pekka, H\u00e4rm\u00e4 Ville, Virtanen Johannes, Sormunen Raija, Kaakinen Mika, Kannala Juho, Eklund Lauri, Heikkil\u00e4 Janne, Nees Matthias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26375443", "url": "https://glygen.org/publication/PubMed/26375443" } ] }, { "title": "CD151-\u03b13\u03b21 integrin complexes are prognostic markers of glioblastoma and cooperate with EGFR to drive tumor cell motility and invasion.", "journal": "Oncotarget", "date": "2015-10-06", "authors": "Zhou Pengcheng, Erfani Sonia, Liu Zeyi, Jia Changhe, Chen Yecang, Xu Bingwei, Deng Xinyu, Alf\u00e1ro Jose E, Chen Li, Napier Dana, Lu Michael, Huang Jian-An, Liu Chunming, Thibault Olivier, Segal Rosalind, Zhou Binhua P, Kyprianou Natasha, Horbinski Craig, Yang Xiuwei H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26377974", "url": "https://glygen.org/publication/PubMed/26377974" } ] }, { "title": "Focal adhesion kinase overexpression and its impact on human osteosarcoma.", "journal": "Oncotarget", "date": "2015-10-13", "authors": "Ren Ke, Lu Xiao, Yao Nan, Chen Yong, Yang Aizhen, Chen Hui, Zhang Jian, Wu Sujia, Shi Xin, Wang Chen, Sun Xiaoliang", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26393679", "url": "https://glygen.org/publication/PubMed/26393679" } ] }, { "title": "Nuclear FAK controls chemokine transcription, Tregs, and evasion of anti-tumor immunity.", "journal": "Cell", "date": "2015-09-24", "authors": "Serrels Alan, Lund Tom, Serrels Bryan, Byron Adam, McPherson Rhoanne C, von Kriegsheim Alexander, G\u00f3mez-Cuadrado Laura, Canel Marta, Muir Morwenna, Ring Jennifer E, Maniati Eleni, Sims Andrew H, Pachter Jonathan A, Brunton Valerie G, Gilbert Nick, Anderton Stephen M, Nibbs Robert J B, Frame Margaret C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26406376", "url": "https://glygen.org/publication/PubMed/26406376" } ] }, { "title": "Novel anticancer agent, SQAP, binds to focal adhesion kinase and modulates its activity.", "journal": "Scientific reports", "date": "2015", "authors": "Izaguirre-Carbonell J, Kawakubo H, Murata H, Tanabe A, Takeuchi T, Kusayanagi T, Tsukuda S, Hirakawa T, Iwabata K, Kanai Y, Ohta K, Miura M, Sakaguchi K, Matsunaga S, Sahara H, Kamisuki S, Sugawara F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26456697", "url": "https://glygen.org/publication/PubMed/26456697" } ] }, { "title": "Combination of heat shock protein 90 and focal adhesion kinase inhibitors synergistically inhibits the growth of non-small cell lung cancer cells.", "journal": "Oncoscience", "date": "2015", "authors": "Webber PJ, Park C, Qui M, Ramalingam SS, Khuri FR, Fu H, Du Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26501082", "url": "https://glygen.org/publication/PubMed/26501082" } ] }, { "title": "A direct interaction between fascin and microtubules contributes to adhesion dynamics and cell migration.", "journal": "Journal of cell science", "date": "2015", "authors": "Villari G, Jayo A, Zanet J, Fitch B, Serrels B, Frame M, Stramer BM, Goult BT, Parsons M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26542021", "url": "https://glygen.org/publication/PubMed/26542021" } ] }, { "title": "Molecular mechanism of fluoroquinolones modulation on corneal fibroblast motility.", "journal": "Experimental eye research", "date": "2016", "authors": "Chen TC, Tsai TY, Chang SW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26546726", "url": "https://glygen.org/publication/PubMed/26546726" } ] }, { "title": "An EGFR/Src-dependent beta4 integrin/FAK complex contributes to malignancy of breast cancer.", "journal": "Scientific reports", "date": "2015", "authors": "Tai YL, Chu PY, Lai IR, Wang MY, Tseng HY, Guan JL, Liou JY, Shen TL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26549523", "url": "https://glygen.org/publication/PubMed/26549523" } ] }, { "title": "Growth-stimulatory activity of TIMP-2 is mediated through c-Src activation followed by activation of FAK, PI3-kinase/AKT, and ERK1/2 independent of MMP inhibition in lung adenocarcinoma cells.", "journal": "Oncotarget", "date": "2015", "authors": "Kim HIe, Lee HS, Kim TH, Lee JS, Lee ST, Lee SJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26556867", "url": "https://glygen.org/publication/PubMed/26556867" } ] }, { "title": "Vinculin Interacts with the Chlamydia Effector TarP Via a Tripartite Vinculin Binding Domain to Mediate Actin Recruitment and Assembly at the Plasma Membrane.", "journal": "Frontiers in cellular and infection microbiology", "date": "2015", "authors": "Thwaites TR, Pedrosa AT, Peacock TP, Carabeo RA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26649283", "url": "https://glygen.org/publication/PubMed/26649283" } ] }, { "title": "NDN is an imprinted tumor suppressor gene that is downregulated in ovarian cancers through genetic and epigenetic mechanisms.", "journal": "Oncotarget", "date": "2016", "authors": "Yang H, Das P, Yu Y, Mao W, Wang Y, Baggerly K, Wang Y, Marquez RT, Bedi A, Liu J, Fishman D, Lu Z, Bast RC Jr", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26689988", "url": "https://glygen.org/publication/PubMed/26689988" } ] }, { "title": "PTP1B triggers integrin-mediated repression of myosin activity and modulates cell contractility.", "journal": "Biology open", "date": "2015-12-23", "authors": "Gonz\u00e1lez Wusener Ana E, Gonz\u00e1lez \u00c1ngela, Nakamura Fumihiko, Arregui Carlos O", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26700725", "url": "https://glygen.org/publication/PubMed/26700725" } ] }, { "title": "Mycosporine-Like Amino Acids Promote Wound Healing through Focal Adhesion Kinase (FAK) and Mitogen-Activated Protein Kinases (MAP Kinases) Signaling Pathway in Keratinocytes.", "journal": "Marine drugs", "date": "2015", "authors": "Choi YH, Yang DJ, Kulkarni A, Moh SH, Kim KW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26703626", "url": "https://glygen.org/publication/PubMed/26703626" } ] }, { "title": "MUC5AC interactions with integrin \u03b24 enhances the migration of lung cancer cells through FAK signaling.", "journal": "Oncogene", "date": "2016-08-04", "authors": "Lakshmanan I, Rachagani S, Hauke R, Krishn S R, Paknikar S, Seshacharyulu P, Karmakar S, Nimmakayala R K, Kaushik G, Johansson S L, Carey G B, Ponnusamy M P, Kaur S, Batra S K, Ganti A K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26751774", "url": "https://glygen.org/publication/PubMed/26751774" } ] }, { "title": "Tyrosine 397 phosphorylation is critical for FAK-promoted Rac1 activation and invasive properties in oral squamous cell carcinoma cells.", "journal": "Laboratory investigation; a journal of technical methods and pathology", "date": "2016", "authors": "Chiu YW, Liou LY, Chen PT, Huang CM, Luo FJ, Hsu YK, Yuan TC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26752742", "url": "https://glygen.org/publication/PubMed/26752742" } ] }, { "title": "Syntenin is expressed in human gliomas and may correlate with tumor migration.", "journal": "Archives of medical science : AMS", "date": "2015", "authors": "Zhong D, Ran J, Zhang X, Tan Y, Chen G, Tang W, Li X, Wang B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26788094", "url": "https://glygen.org/publication/PubMed/26788094" } ] }, { "title": "Kindlin-2 cooperates with talin to activate integrins and induces cell spreading by directly binding paxillin.", "journal": "eLife", "date": "2016", "authors": "Theodosiou M, Widmaier M, Bottcher RT, Rognoni E, Veelders M, Bharadwaj M, Lambacher A, Austen K, Muller DJ, Zent R, Fassler R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26821125", "url": "https://glygen.org/publication/PubMed/26821125" } ] }, { "title": "Modulation of FAK and Src adhesion signaling occurs independently of adhesion complex composition.", "journal": "The Journal of cell biology", "date": "2016", "authors": "Horton ER, Humphries JD, Stutchbury B, Jacquemet G, Ballestrem C, Barry ST, Humphries MJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26833789", "url": "https://glygen.org/publication/PubMed/26833789" } ] }, { "title": "The FAK-Arp2/3 interaction promotes leading edge advance and haptosensing by coupling nascent adhesions to lamellipodia actin.", "journal": "Molecular biology of the cell", "date": "2016-04-01", "authors": "Swaminathan Vinay, Fischer R S, Waterman Clare M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26842895", "url": "https://glygen.org/publication/PubMed/26842895" } ] }, { "title": "Reelin promotes the adhesion and drug resistance of multiple myeloma cells via integrin beta1 signaling and STAT3.", "journal": "Oncotarget", "date": "2016", "authors": "Lin L, Yan F, Zhao D, Lv M, Liang X, Dai H, Qin X, Zhang Y, Hao J, Sun X, Yin Y, Huang X, Zhang J, Lu J, Ge Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26848618", "url": "https://glygen.org/publication/PubMed/26848618" } ] }, { "title": "Novel Role of Src in Priming Pyk2 Phosphorylation.", "journal": "PloS one", "date": "2016", "authors": "Zhao M, Finlay D, Zharkikh I, Vuori K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" } ] }, { "title": "Expression of pY397 FAK promotes the development of non-small cell lung cancer.", "journal": "Oncology letters", "date": "2016", "authors": "Wang B, Qi X, Li D, Feng M, Meng X, Fu S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26893679", "url": "https://glygen.org/publication/PubMed/26893679" } ] }, { "title": "Cathepsin K induces platelet dysfunction and affects cell signaling in breast cancer - molecularly distinct behavior of cathepsin K in breast cancer.", "journal": "BMC cancer", "date": "2016-03-01", "authors": "Andrade Sheila Siqueira, Gouvea Iuri Estrada, Silva Mariana Cristina C, Castro Elo\u00edsa Dognani, de Paula Cl\u00e1udia A A, Okamoto Debora, Oliveira Lilian, Peres Giovani Bravin, Ottaiano Tatiana, Facina Gil, Naz\u00e1rio Afonso Celso Pinto, Campos Antonio Hugo J F M, Paredes-Gamero Edgar Julian, Juliano Maria, da Silva Ismael D C G, Oliva Maria Luiza V, Gir\u00e3o Manoel J B C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26931461", "url": "https://glygen.org/publication/PubMed/26931461" } ] }, { "title": "Inhibition of adhesion, migration and of alpha5beta1 integrin in the HCT-116 colorectal cancer cells treated with the ruthenium drug NAMI-A.", "journal": "Journal of inorganic biochemistry", "date": "2016", "authors": "Pelillo C, Mollica H, Eble JA, Grosche J, Herzog L, Codan B, Sava G, Bergamo A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26961176", "url": "https://glygen.org/publication/PubMed/26961176" } ] }, { "title": "Loss of miR-203 regulates cell shape and matrix adhesion through ROBO1/Rac/FAK in response to stiffness.", "journal": "The Journal of cell biology", "date": "2016", "authors": "Le LT, Cazares O, Mouw JK, Chatterjee S, Macias H, Moran A, Ramos J, Keely PJ, Weaver VM, Hinck L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26975850", "url": "https://glygen.org/publication/PubMed/26975850" } ] }, { "title": "FAK tyrosine 407 organized with integrin \u03b1V\u03b25 in Hs578Ts(i)8 advanced triple-negative breast cancer cells.", "journal": "International journal of oncology", "date": "2016-05", "authors": "Payan Iliet, McDonnell Susan, Torres Haydee M, Steelant Wim F A, Van Slambrouck S\u00e9verine", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26984508", "url": "https://glygen.org/publication/PubMed/26984508" } ] }, { "title": "Nuclear expression of Lyn, a Src family kinase member, is associated with poor prognosis in renal cancer patients.", "journal": "BMC cancer", "date": "2016", "authors": "Roseweir AK, Qayyum T, Lim Z, Hammond R, MacDonald AI, Fraser S, Oades GM, Aitchison M, Jones RJ, Edwards J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26984511", "url": "https://glygen.org/publication/PubMed/26984511" } ] }, { "title": "Fluvoxamine, an anti-depressant, inhibits human glioblastoma invasion by disrupting actin polymerization.", "journal": "Scientific reports", "date": "2016", "authors": "Hayashi K, Michiue H, Yamada H, Takata K, Nakayama H, Wei FY, Fujimura A, Tazawa H, Asai A, Ogo N, Miyachi H, Nishiki T, Tomizawa K, Takei K, Matsui H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26988603", "url": "https://glygen.org/publication/PubMed/26988603" } ] }, { "title": "Kruppel-like factor 8 activates the transcription of C-X-C cytokine receptor type 4 to promote breast cancer cell invasion, transendothelial migration and metastasis.", "journal": "Oncotarget", "date": "2016", "authors": "Mukherjee D, Lu H, Yu L, He C, Lahiri SK, Li T, Zhao J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26993780", "url": "https://glygen.org/publication/PubMed/26993780" } ] }, { "title": "Therapeutic effects of tyroservatide on metastasis of lung cancer and its mechanism affecting integrin-focal adhesion kinase signal transduction.", "journal": "Drug design, development and therapy", "date": "2016", "authors": "Huang YT, Zhao L, Fu Z, Zhao M, Song XM, Jia J, Wang S, Li JP, Zhu ZF, Lin G, Lu R, Yao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" } ] }, { "title": "Sulfatide interacts with and activates integrin \u03b1V\u03b23 in human hepatocellular carcinoma cells.", "journal": "Oncotarget", "date": "2016-06-14", "authors": "Wang Rong, Qi Bing, Dong Yi Wei, Cai Qian Qian, Deng Nian Hui, Chen Qi, Li Chao, Jin Yu Tong, Wu Xing Zhong", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276" } ] }, { "title": "Notch1 pathway-mediated microRNA-151-5p promotes gastric cancer progression.", "journal": "Oncotarget", "date": "2016-06-21", "authors": "Hsu Kai-Wen, Fang Wen-Liang, Huang Kuo-Hung, Huang Tzu-Ting, Lee Hsin-Chen, Hsieh Rong-Hong, Chi Chin-Wen, Yeh Tien-Shun", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27191259", "url": "https://glygen.org/publication/PubMed/27191259" } ] }, { "title": "The effect of soluble E-selectin on tumor progression and metastasis.", "journal": "BMC cancer", "date": "2016", "authors": "Kang SA, Blache CA, Bajana S, Hasan N, Kamal M, Morita Y, Gupta V, Tsolmon B, Suh KS, Gorenstein DG, Razaq W, Rui H, Tanaka T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27220365", "url": "https://glygen.org/publication/PubMed/27220365" } ] }, { "title": "PIAS1-FAK Interaction Promotes the Survival and Progression of Non-Small Cell Lung Cancer.", "journal": "Neoplasia (New York, N.Y.)", "date": "2016", "authors": "Constanzo JD, Tang KJ, Rindhe S, Melegari M, Liu H, Tang X, Rodriguez-Canales J, Wistuba I, Scaglioni PP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27237320", "url": "https://glygen.org/publication/PubMed/27237320" } ] }, { "title": "The SHIP2 interactor Myo1c is required for cell migration in 1321 N1 glioblastoma cells.", "journal": "Biochemical and biophysical research communications", "date": "2016", "authors": "Edimo WE, Ramos AR, Ghosh S, Vanderwinden JM, Erneux C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27246739", "url": "https://glygen.org/publication/PubMed/27246739" } ] }, { "title": "AKR1B10 promotes breast cancer metastasis through integrin alpha5/delta-catenin mediated FAK/Src/Rac1 signaling pathway.", "journal": "Oncotarget", "date": "2016", "authors": "Huang C, Verhulst S, Shen Y, Bu Y, Cao Y, He Y, Wang Y, Huang D, Cai C, Rao K, Liao DF, Jin J, Cao D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27248472", "url": "https://glygen.org/publication/PubMed/27248472" } ] }, { "title": "Pigment epithelium-derived factor (PEDF): a novel trophoblast-derived factor limiting feto-placental angiogenesis in late pregnancy.", "journal": "Angiogenesis", "date": "2016", "authors": "Loegl J, Nussbaumer E, Hiden U, Majali-Martinez A, Ghaffari-Tabrizi-Wizy N, Cvitic S, Lang I, Desoye G, Huppertz B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27278471", "url": "https://glygen.org/publication/PubMed/27278471" } ] }, { "title": "HER2 reduces breast cancer radiosensitivity by activating focal adhesion kinase in vitro and in vivo.", "journal": "Oncotarget", "date": "2016", "authors": "Hou J, Zhou Z, Chen X, Zhao R, Yang Z, Wei N, Ni Q, Feng Y, Yu X, Ma J, Guo X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256" } ] }, { "title": "Prolactin signaling through focal adhesion complexes is amplified by stiff extracellular matrices in breast cancer cells.", "journal": "Oncotarget", "date": "2016-07-26", "authors": "Barcus Craig E, Keely Patricia J, Eliceiri Kevin W, Schuler Linda A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27344177", "url": "https://glygen.org/publication/PubMed/27344177" } ] }, { "title": "Crizotinib inhibits NF2-associated schwannoma through inhibition of focal adhesion kinase 1.", "journal": "Oncotarget", "date": "2016-08-23", "authors": "Troutman Scott, Moleirinho Susana, Kota Smitha, Nettles Kendall, Fallahi Mohammad, Johnson Gary L, Kissil Joseph L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27363027", "url": "https://glygen.org/publication/PubMed/27363027" } ] }, { "title": "Focal adhesion kinase is required for actin polymerization and remodeling of the cytoskeleton during sperm capacitation.", "journal": "Biology open", "date": "2016", "authors": "Roa-Espitia AL, Hernandez-Rendon ER, Baltierrez-Hoyos R, Munoz-Gotera RJ, Cote-Velez A, Jimenez I, Gonzalez-Marquez H, Hernandez-Gonzalez EO", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27402964", "url": "https://glygen.org/publication/PubMed/27402964" } ] }, { "title": "A Role for Focal Adhesion Kinase in the Stimulation of Glucose Transport in Cardiomyocytes.", "journal": "Journal of cellular biochemistry", "date": "2017", "authors": "Viglino C, Montessuit C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27428469", "url": "https://glygen.org/publication/PubMed/27428469" } ] }, { "title": "Neutral endopeptidase (NEP) is differentially involved in biological activities and cell signaling of colon cancer cell lines derived from various stages of tumor development.", "journal": "Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine", "date": "2016", "authors": "Mizerska-Kowalska M, Bojarska-Junak A, Jakubowicz-Gil J, Kandefer-Szerszen M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27460083", "url": "https://glygen.org/publication/PubMed/27460083" } ] }, { "title": "MIEN1 drives breast tumor cell migration by regulating cytoskeletal-focal adhesion dynamics.", "journal": "Oncotarget", "date": "2016", "authors": "Kpetemey M, Chaudhary P, Van Treuren T, Vishwanatha JK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27462783", "url": "https://glygen.org/publication/PubMed/27462783" } ] }, { "title": "Impact of shear stress on Src and focal adhesion kinase phosphorylation in fibrinogen-adherent platelets.", "journal": "Blood coagulation & fibrinolysis : an international journal in haemostasis and thrombosis", "date": "2017", "authors": "Huynh KC, Gyenes M, Nguyen TH, Vo TV, Stoldt VR", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27467982", "url": "https://glygen.org/publication/PubMed/27467982" } ] }, { "title": "Integrin alphaVbeta3 silencing sensitizes malignant glioma cells to temozolomide by suppression of homologous recombination repair.", "journal": "Oncotarget", "date": "2017", "authors": "Christmann M, Diesler K, Majhen D, Steigerwald C, Berte N, Freund H, Stojanovic N, Kaina B, Osmak M, Ambriovic-Ristov A, Tomicic MT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27487141", "url": "https://glygen.org/publication/PubMed/27487141" } ] }, { "title": "Prolactin-induced PAK1 tyrosyl phosphorylation promotes FAK dephosphorylation, breast cancer cell motility, invasion and metastasis.", "journal": "BMC cell biology", "date": "2016", "authors": "Hammer A, Diakonova M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27542844", "url": "https://glygen.org/publication/PubMed/27542844" } ] }, { "title": "Targeting Focal Adhesion Kinase Suppresses the Malignant Phenotype in Rhabdomyosarcoma Cells.", "journal": "Translational oncology", "date": "2016-08", "authors": "Waters Alicia M, Stafman Laura L, Garner Evan F, Mruthyunjayappa Smitha, Stewart Jerry E, Mroczek-Musulman Elizabeth, Beierle Elizabeth A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27567948", "url": "https://glygen.org/publication/PubMed/27567948" } ] }, { "title": "Thrombomodulin promotes focal adhesion kinase activation and contributes to angiogenesis by binding to fibronectin.", "journal": "Oncotarget", "date": "2016", "authors": "Hsu YY, Shi GY, Wang KC, Ma CY, Cheng TL, Wu HL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27602495", "url": "https://glygen.org/publication/PubMed/27602495" } ] }, { "title": "Oncogenic activation of FAK drives apoptosis suppression in a 3D-culture model of breast cancer initiation.", "journal": "Oncotarget", "date": "2016", "authors": "Walker S, Foster F, Wood A, Owens T, Brennan K, Streuli CH, Gilmore AP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27611942", "url": "https://glygen.org/publication/PubMed/27611942" } ] }, { "title": "Oncogenic Receptor Tyrosine Kinases Directly Phosphorylate Focal Adhesion Kinase (FAK) as a Resistance Mechanism to FAK-Kinase Inhibitors.", "journal": "Molecular cancer therapeutics", "date": "2016-12", "authors": "Marlowe Timothy A, Lenzo Felicia L, Figel Sheila A, Grapes Abigail T, Cance William G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27638858", "url": "https://glygen.org/publication/PubMed/27638858" } ] }, { "title": "Orphan G protein-coupled receptor GPRC5A modulates integrin beta1-mediated epithelial cell adhesion.", "journal": "Cell adhesion & migration", "date": "2017", "authors": "Bulanova DR, Akimov YA, Rokka A, Laajala TD, Aittokallio T, Kouvonen P, Pellinen T, Kuznetsov SG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27715394", "url": "https://glygen.org/publication/PubMed/27715394" } ] }, { "title": "Cancer derived peptide of vacuolar ATPase 'a2' isoform promotes neutrophil migration by autocrine secretion of IL-8.", "journal": "Scientific reports", "date": "2016", "authors": "Ibrahim SA, Kulshrestha A, Katara GK, Amin MA, Beaman KD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27845385", "url": "https://glygen.org/publication/PubMed/27845385" } ] }, { "title": "Vincristine alleviates adriamycin-induced nephropathy through stabilizing actin cytoskeleton.", "journal": "Cell & bioscience", "date": "2017", "authors": "Yin L, Mao Y, Song H, Wang Y, Zhou W, Zhang Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28053698", "url": "https://glygen.org/publication/PubMed/28053698" } ] }, { "title": "Enterolactone alters FAK-Src signaling and suppresses migration and invasion of lung cancer cell lines.", "journal": "BMC complementary and alternative medicine", "date": "2017", "authors": "Chikara S, Lindsey K, Borowicz P, Christofidou-Solomidou M, Reindl KM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28068967", "url": "https://glygen.org/publication/PubMed/28068967" } ] }, { "title": "Aeroallergen Der p 2 promotes motility of human non-small cell lung cancer cells via toll-like receptor-mediated up-regulation of urokinase-type plasminogen activator and integrin/focal adhesion kinase signaling.", "journal": "Oncotarget", "date": "2017", "authors": "Lin CH, Lin HH, Kuo CY, Kao SH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28076322", "url": "https://glygen.org/publication/PubMed/28076322" } ] }, { "title": "Structural Insights How PIP2 Imposes Preferred Binding Orientations of FAK at Lipid Membranes.", "journal": "The journal of physical chemistry. B", "date": "2017", "authors": "Herzog FA, Braun L, Schoen I, Vogel V", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28124908", "url": "https://glygen.org/publication/PubMed/28124908" } ] }, { "title": "Inhibition of the integrin/FAK signaling axis and c-Myc synergistically disrupts ovarian cancer malignancy.", "journal": "Oncogenesis", "date": "2017", "authors": "Xu B, Lefringhouse J, Liu Z, West D, Baldwin LA, Ou C, Chen L, Napier D, Chaiswing L, Brewer LD, St Clair D, Thibault O, van Nagell JR, Zhou BP, Drapkin R, Huang JA, Lu ML, Ueland FR, Yang XH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28134933", "url": "https://glygen.org/publication/PubMed/28134933" } ] }, { "title": "Tetraspanin 8 is a novel regulator of ILK-driven beta1 integrin adhesion and signaling in invasive melanoma cells.", "journal": "Oncotarget", "date": "2017", "authors": "El Kharbili M, Robert C, Witkowski T, Danty-Berger E, Barbollat-Boutrand L, Masse I, Gadot N, de la Fouchardiere A, McDonald PC, Dedhar S, Le Naour F, Degoul F, Berthier-Vergnes O", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28188308", "url": "https://glygen.org/publication/PubMed/28188308" } ] }, { "title": "Phospholipid binding to the FAK catalytic domain impacts function.", "journal": "PloS one", "date": "2017", "authors": "Hall Jessica E, Schaller Michael D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177" } ] }, { "title": "Targeted inhibition of Focal Adhesion Kinase Attenuates Cardiac Fibrosis and Preserves Heart Function in Adverse Cardiac Remodeling.", "journal": "Scientific reports", "date": "2017", "authors": "Zhang J, Fan G, Zhao H, Wang Z, Li F, Zhang P, Zhang J, Wang X, Wang W", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28225063", "url": "https://glygen.org/publication/PubMed/28225063" } ] }, { "title": "RNase L Suppresses Androgen Receptor Signaling, Cell Migration and Matrix Metalloproteinase Activity in Prostate Cancer Cells.", "journal": "International journal of molecular sciences", "date": "2017-03-01", "authors": "Dayal Shubham, Zhou Jun, Manivannan Praveen, Siddiqui Mohammad Adnan, Ahmad Omaima Farid, Clark Matthew, Awadia Sahezeel, Garcia-Mata Rafael, Shemshedini Lirim, Malathi Krishnamurthy", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28257035", "url": "https://glygen.org/publication/PubMed/28257035" } ] }, { "title": "Focal adhesion kinase depletion reduces human hepatocellular carcinoma growth by repressing enhancer of zeste homolog 2.", "journal": "Cell death and differentiation", "date": "2017", "authors": "Gnani D, Romito I, Artuso S, Chierici M, De Stefanis C, Panera N, Crudele A, Ceccarelli S, Carcarino E, D'Oria V, Porru M, Giorda E, Ferrari K, Miele L, Villa E, Balsano C, Pasini D, Furlanello C, Locatelli F, Nobili V, Rota R, Leonetti C, Alisi A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28338656", "url": "https://glygen.org/publication/PubMed/28338656" } ] }, { "title": "PCTK3/CDK18 regulates cell migration and adhesion by negatively modulating FAK activity.", "journal": "Scientific reports", "date": "2017", "authors": "Matsuda S, Kawamoto K, Miyamoto K, Tsuji A, Yuasa K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28361970", "url": "https://glygen.org/publication/PubMed/28361970" } ] }, { "title": "Kctd20 promotes the development of non-small cell lung cancer through activating Fak/AKT pathway and predicts poor overall survival of patients.", "journal": "Molecular carcinogenesis", "date": "2017", "authors": "Zhang X, Zhou H, Cai L, Fan C, Liu Y, Wang L, Li Q, Miao Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28398603", "url": "https://glygen.org/publication/PubMed/28398603" } ] }, { "title": "Antitumor effect of focal adhesion kinase inhibitor PF562271 against human osteosarcoma in vitro and in vivo.", "journal": "Cancer science", "date": "2017", "authors": "Hu C, Chen X, Wen J, Gong L, Liu Z, Wang J, Liang J, Hu F, Zhou Q, Wei L, Shen Y, Zhang W", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28406574", "url": "https://glygen.org/publication/PubMed/28406574" } ] }, { "title": "miR-135a inhibits tumor metastasis and angiogenesis by targeting FAK pathway.", "journal": "Oncotarget", "date": "2017", "authors": "Cheng Z, Liu F, Zhang H, Li X, Li Y, Li J, Liu F, Cao Y, Cao L, Li F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28415713", "url": "https://glygen.org/publication/PubMed/28415713" } ] }, { "title": "Kinomic profiling identifies focal adhesion kinase 1 as a therapeutic target in advanced clear cell renal cell carcinoma.", "journal": "Oncotarget", "date": "2017-04-25", "authors": "Ghosh Arindam P, Willey Christopher D, Anderson Joshua C, Welaya Karim, Chen Dongquan, Mehta Amitkumar, Ghatalia Pooja, Madan Ankit, Naik Gurudatta, Sudarshan Sunil, Sonpavde Guru", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903" } ] }, { "title": "Procollagen-lysine 2-oxoglutarate 5-dioxygenase 2 promotes hypoxia-induced glioma migration and invasion.", "journal": "Oncotarget", "date": "2017", "authors": "Xu Y, Zhang L, Wei Y, Zhang X, Xu R, Han M, Huang B, Chen A, Li W, Zhang Q, Li G, Wang J, Zhao P, Li X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28423580", "url": "https://glygen.org/publication/PubMed/28423580" } ] }, { "title": "Ponatinib promotes a G1 cell-cycle arrest of merlin/NF2-deficient human schwann cells.", "journal": "Oncotarget", "date": "2017", "authors": "Petrilli AM, Garcia J, Bott M, Klingeman Plati S, Dinh CT, Bracho OR, Yan D, Zou B, Mittal R, Telischi FF, Liu XZ, Chang LS, Welling DB, Copik AJ, Fernandez-Valle C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224" } ] }, { "title": "FAK phosphorylation plays a central role in thrombin-induced RPE cell migration.", "journal": "Cellular signalling", "date": "2017", "authors": "Aguilar-Solis ED, Lee-Rivera I, Alvarez-Arce A, Lopez E, Lopez-Colome AM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28445805", "url": "https://glygen.org/publication/PubMed/28445805" } ] }, { "title": "Endoglin Mediates Vascular Maturation by Promoting Vascular Smooth Muscle Cell Migration and Spreading.", "journal": "Arteriosclerosis, thrombosis, and vascular biology", "date": "2017", "authors": "Tian H, Ketova T, Hardy D, Xu X, Gao X, Zijlstra A, Blobe GC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28450296", "url": "https://glygen.org/publication/PubMed/28450296" } ] }, { "title": "Metformin inhibits SUV39H1-mediated migration of prostate cancer cells.", "journal": "Oncogenesis", "date": "2017", "authors": "Yu T, Wang C, Yang J, Guo Y, Wu Y, Li X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28459432", "url": "https://glygen.org/publication/PubMed/28459432" } ] }, { "title": "Integrin beta8 (ITGB8) activates VAV-RAC1 signaling via FAK in the acquisition of endometrial epithelial cell receptivity for blastocyst implantation.", "journal": "Scientific reports", "date": "2017", "authors": "Kumar V, Soni UK, Maurya VK, Singh K, Jha RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28507287", "url": "https://glygen.org/publication/PubMed/28507287" } ] }, { "title": "Binding of CIB1 to the alphaIIb tail of alphaIIbbeta3 is required for FAK recruitment and activation in platelets.", "journal": "PloS one", "date": "2017", "authors": "Naik MU, Naik TU, Summer R, Naik UP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28542214", "url": "https://glygen.org/publication/PubMed/28542214" } ] }, { "title": "TRIB1 promotes colorectal cancer cell migration and invasion through activation MMP-2 via FAK/Src and ERK pathways.", "journal": "Oncotarget", "date": "2017-07-18", "authors": "Wang Yuhui, Wu Nan, Pang Bo, Tong Dandan, Sun Donglin, Sun Haiming, Zhang Chunyu, Sun Wenjing, Meng Xiangning, Bai Jing, Chen Feng, Geng Jingshu, Fu Songbin, Jin Yan", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28624785", "url": "https://glygen.org/publication/PubMed/28624785" } ] }, { "title": "Focal Adhesion Kinase Regulates Hepatic Stellate Cell Activation and Liver Fibrosis.", "journal": "Scientific reports", "date": "2017", "authors": "Zhao XK, Yu L, Cheng ML, Che P, Lu YY, Zhang Q, Mu M, Li H, Zhu LL, Zhu JJ, Hu M, Li P, Liang YD, Luo XH, Cheng YJ, Xu ZX, Ding Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28642549", "url": "https://glygen.org/publication/PubMed/28642549" } ] }, { "title": "Lasp2 enhances tumor invasion via facilitating phosphorylation of FAK and predicts poor overall survival of non-small cell lung cancer patients.", "journal": "Molecular carcinogenesis", "date": "2017", "authors": "Zhang X, Cai L, Zhou H, Liu Y, Fan C, Wang L, Li A, Miao Y, Li Q, Qiu X, Wang E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28667800", "url": "https://glygen.org/publication/PubMed/28667800" } ] }, { "title": "Engineered extracellular matrices with controlled mechanics modulate renal proximal tubular cell epithelialization.", "journal": "PloS one", "date": "2017", "authors": "Beamish JA, Chen E, Putnam AJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28715434", "url": "https://glygen.org/publication/PubMed/28715434" } ] }, { "title": "Diallyl trisulfide inhibits cell migration and invasion of human melanoma a375 cells via inhibiting integrin/facal adhesion kinase pathway.", "journal": "Environmental toxicology", "date": "2017", "authors": "Wang HC, Chu YL, Hsieh SC, Sheen LY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28741790", "url": "https://glygen.org/publication/PubMed/28741790" } ] }, { "title": "Collagen triple helix repeat containing 1 (CTHRC1) activates Integrin beta3/FAK signaling and promotes metastasis in ovarian cancer.", "journal": "Journal of ovarian research", "date": "2017", "authors": "Guo B, Yan H, Li L, Yin K, Ji F, Zhang S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29021002", "url": "https://glygen.org/publication/PubMed/29021002" } ] }, { "title": "Toxoplasma gondii induces FAK-Src-STAT3 signaling during infection of host cells that prevents parasite targeting by autophagy.", "journal": "PLoS pathogens", "date": "2017-10", "authors": "Portillo Jose-Andres C, Muniz-Feliciano Luis, Lopez Corcino Yalitza, Lee So Jung, Van Grol Jennifer, Parsons Sarah J, Schiemman William P, Subauste Carlos S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29036202", "url": "https://glygen.org/publication/PubMed/29036202" } ] }, { "title": "Black rice-derived anthocyanins inhibit HER-2-positive breast cancer epithelial-mesenchymal transition-mediated metastasis in vitro by suppressing FAK signaling.", "journal": "International journal of molecular medicine", "date": "2017", "authors": "Zhou J, Zhu YF, Chen XY, Han B, Li F, Chen JY, Peng XL, Luo LP, Chen W, Yu XP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29039492", "url": "https://glygen.org/publication/PubMed/29039492" } ] }, { "title": "Epithelial contribution to the profibrotic stiff microenvironment and myofibroblast population in lung fibrosis.", "journal": "Molecular biology of the cell", "date": "2017", "authors": "Gabasa M, Duch P, Jorba I, Gimenez A, Lugo R, Pavelescu I, Rodriguez-Pascual F, Molina-Molina M, Xaubet A, Pereda J, Alcaraz J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29046395", "url": "https://glygen.org/publication/PubMed/29046395" } ] }, { "title": "The activation of SRC family kinases and focal adhesion kinase with the loss of the amplified, mutated EGFR gene contributes to the resistance to afatinib, erlotinib and osimertinib in human lung cancer cells.", "journal": "Oncotarget", "date": "2017", "authors": "Murakami Y, Sonoda K, Abe H, Watari K, Kusakabe D, Azuma K, Kawahara A, Akiba J, Oneyama C, Pachter JA, Sakai K, Nishio K, Kuwano M, Ono M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" } ] }, { "title": "Phosphoinositide-specific phospholipase Cgamma1 inhibition induces autophagy in human colon cancer and hepatocellular carcinoma cells.", "journal": "Scientific reports", "date": "2017", "authors": "Dai L, Chen X, Lu X, Wang F, Zhan Y, Song G, Hu T, Xia C, Zhang B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29066806", "url": "https://glygen.org/publication/PubMed/29066806" } ] }, { "title": "Lasp1 promotes malignant phenotype of non-small-cell lung cancer via inducing phosphorylation of FAK-AKT pathway.", "journal": "Oncotarget", "date": "2017", "authors": "Zhang X, Liu Y, Fan C, Wang L, Li A, Zhou H, Cai L, Miao Y, Li Q, Qiu X, Wang E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29088849", "url": "https://glygen.org/publication/PubMed/29088849" } ] }, { "title": "Insufficient Radiofrequency Ablation Treated Hepatocellular Carcinoma Cells Promote Metastasis by Up-Regulation ITGB3.", "journal": "Journal of Cancer", "date": "2017", "authors": "Zhang N, Ma D, Wang L, Zhu X, Pan Q, Zhao Y, Zhu W, Zhou J, Wang L, Chai Z, Ao J, Sun H, Tang Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29151962", "url": "https://glygen.org/publication/PubMed/29151962" } ] }, { "title": "Activation of Rho-kinase and focal adhesion kinase regulates the organization of stress fibers and focal adhesions in the central part of fibroblasts.", "journal": "PeerJ", "date": "2017", "authors": "Katoh Kazuo", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29158989", "url": "https://glygen.org/publication/PubMed/29158989" } ] }, { "title": "Effect of Clinically Relevant CAD/CAM Zirconia Polishing on Gingival Fibroblast Proliferation and Focal Adhesions.", "journal": "Materials (Basel, Switzerland)", "date": "2017", "authors": "Fischer NG, Wong J, Baruth A, Cerutis DR", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29186907", "url": "https://glygen.org/publication/PubMed/29186907" } ] }, { "title": "FUS-CHOP Promotes Invasion in Myxoid Liposarcoma through a SRC/FAK/RHO/ROCK-Dependent Pathway.", "journal": "Neoplasia (New York, N.Y.)", "date": "2018", "authors": "Tornin J, Hermida-Prado F, Padda RS, Gonzalez MV, Alvarez-Fernandez C, Rey V, Martinez-Cruzado L, Estupinan O, Menendez ST, Fernandez-Nevado L, Astudillo A, Rodrigo JP, Lucien F, Kim Y, Leong HS, Garcia-Pedrero JM, Rodriguez R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29190494", "url": "https://glygen.org/publication/PubMed/29190494" } ] }, { "title": "Inhibition of pressure-activated cancer cell adhesion by FAK-derived peptides.", "journal": "Oncotarget", "date": "2017", "authors": "Zeng B, Devadoss D, Wang S, Vomhof-DeKrey EE, Kuhn LA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29228673", "url": "https://glygen.org/publication/PubMed/29228673" } ] }, { "title": "Chemotherapy induces ovarian cancer cell repopulation through the caspase 3-mediated arachidonic acid metabolic pathway.", "journal": "OncoTargets and therapy", "date": "2017", "authors": "Cui L, Zhao Y, Pan Y, Zheng X, Shao D, Jia Y, He K, Li K, Chen L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29263678", "url": "https://glygen.org/publication/PubMed/29263678" } ] }, { "title": "ZNF259 inhibits non-small cell lung cancer cells proliferation and invasion by FAK-AKT signaling.", "journal": "Cancer management and research", "date": "2017", "authors": "Shan Y, Cao W, Wang T, Jiang G, Zhang Y, Yang X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29276408", "url": "https://glygen.org/publication/PubMed/29276408" } ] }, { "title": "Src- and confinement-dependent FAK activation causes E-cadherin relaxation and beta-catenin activity.", "journal": "The Journal of cell biology", "date": "2018", "authors": "Gayrard C, Bernaudin C, Dejardin T, Seiler C, Borghi N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29311227", "url": "https://glygen.org/publication/PubMed/29311227" } ] }, { "title": "Integrin-uPAR signaling leads to FRA-1 phosphorylation and enhanced breast cancer invasion.", "journal": "Breast cancer research : BCR", "date": "2018", "authors": "Annis MG, Ouellet V, Rennhack JP, L'Esperance S, Rancourt C, Mes-Masson AM, Andrechek ER, Siegel PM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29382358", "url": "https://glygen.org/publication/PubMed/29382358" } ] }, { "title": "Cx26 drives self-renewal in triple-negative breast cancer via interaction with NANOG and focal adhesion kinase.", "journal": "Nature communications", "date": "2018", "authors": "Thiagarajan PS, Sinyuk M, Turaga SM, Mulkearns-Hubert EE, Hale JS, Rao V, Demelash A, Saygin C, China A, Alban TJ, Hitomi M, Torre-Healy LA, Alvarado AG, Jarrar A, Wiechert A, Adorno-Cruz V, Fox PL, Calhoun BC, Guan JL, Liu H, Reizes O, Lathia JD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29422613", "url": "https://glygen.org/publication/PubMed/29422613" } ] }, { "title": "Sodium butyrate induces senescence and inhibits the invasiveness of glioblastoma cells.", "journal": "Oncology letters", "date": "2018", "authors": "Nakagawa H, Sasagawa S, Itoh K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29434841", "url": "https://glygen.org/publication/PubMed/29434841" } ] }, { "title": "Impact of PKCepsilon downregulation on autophagy in glioblastoma cells.", "journal": "BMC cancer", "date": "2018", "authors": "Toton E, Romaniuk A, Konieczna N, Hofmann J, Barciszewski J, Rybczynska M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667" } ] }, { "title": "Inhibition of cell migration by focal adhesion kinase: Time-dependent difference in integrin-induced signaling between endothelial and hepatoblastoma cells.", "journal": "International journal of molecular medicine", "date": "2018", "authors": "Yu H, Gao M, Ma Y, Wang L, Shen Y, Liu X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29484384", "url": "https://glygen.org/publication/PubMed/29484384" } ] }, { "title": "Simulated microgravity inhibits cell focal adhesions leading to reduced melanoma cell proliferation and metastasis via FAK/RhoA-regulated mTORC1 and AMPK pathways.", "journal": "Scientific reports", "date": "2018", "authors": "Tan X, Xu A, Zhao T, Zhao Q, Zhang J, Fan C, Deng Y, Freywald A, Genth H, Xiang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29491429", "url": "https://glygen.org/publication/PubMed/29491429" } ] }, { "title": "The KDEL receptor signalling cascade targets focal adhesion kinase on focal adhesions and invadopodia.", "journal": "Oncotarget", "date": "2018", "authors": "Ruggiero C, Grossi M, Fragassi G, Di Campli A, Di Ilio C, Luini A, Sallese M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29535802", "url": "https://glygen.org/publication/PubMed/29535802" } ] }, { "title": "The Role of FAK in the Secretion of MMP9 after CD147 Stimulation in Macrophages.", "journal": "International heart journal", "date": "2018", "authors": "Yu C, Lixia Y, Ruiwei G, Yankun S, Jinshan Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29563383", "url": "https://glygen.org/publication/PubMed/29563383" } ] }, { "title": "Apigenin and Luteolin Attenuate the Breaching of MDA-MB231 Breast Cancer Spheroids Through the Lymph Endothelial Barrier in Vitro.", "journal": "Frontiers in pharmacology", "date": "2018", "authors": "Hong J, Fristiohady A, Nguyen CH, Milovanovic D, Huttary N, Krieger S, Hong J, Geleff S, Birner P, Jager W, Ozmen A, Krenn L, Krupitza G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29593542", "url": "https://glygen.org/publication/PubMed/29593542" } ] }, { "title": "RCP induces FAK phosphorylation and ovarian cancer cell invasion with inhibition by curcumin.", "journal": "Experimental & molecular medicine", "date": "2018", "authors": "Choe SR, Kim YN, Park CG, Cho KH, Cho DY, Lee HY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29700289", "url": "https://glygen.org/publication/PubMed/29700289" } ] }, { "title": "Neuropilin-1 promotes the oncogenic Tenascin-C/integrin beta3 pathway and modulates chemoresistance in breast cancer cells.", "journal": "BMC cancer", "date": "2018", "authors": "Naik A, Al-Yahyaee A, Abdullah N, Sam JE, Al-Zeheimi N, Yaish MW, Adham SA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29728077", "url": "https://glygen.org/publication/PubMed/29728077" } ] }, { "title": "The mechanical microenvironment regulates ovarian cancer cell morphology, migration, and spheroid disaggregation.", "journal": "Scientific reports", "date": "2018", "authors": "McKenzie AJ, Hicks SR, Svec KV, Naughton H, Edmunds ZL, Howe AK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29740072", "url": "https://glygen.org/publication/PubMed/29740072" } ] }, { "title": "PTBP3 contributes to the metastasis of gastric cancer by mediating CAV1 alternative splicing.", "journal": "Cell death & disease", "date": "2018", "authors": "Liang X, Chen W, Shi H, Gu X, Li Y, Qi Y, Xu K, Zhao A, Liu J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29752441", "url": "https://glygen.org/publication/PubMed/29752441" } ] }, { "title": "Human soluble phospholipase A2 receptor is an inhibitor of the integrin-mediated cell migratory response to collagen-I.", "journal": "American journal of physiology. Cell physiology", "date": "2018", "authors": "Watanabe K, Watanabe K, Watanabe Y, Fujioka D, Nakamura T, Nakamura K, Obata JE, Kugiyama K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29791208", "url": "https://glygen.org/publication/PubMed/29791208" } ] }, { "title": "Differential prognostic impact of interleukin-34 mRNA expression and infiltrating immune cell composition in intrinsic breast cancer subtypes.", "journal": "Oncotarget", "date": "2018-05-01", "authors": "Zins Karin, Heller Gerwin, Mayerhofer Mathias, Schreiber Martin, Abraham Dietmar", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29796177", "url": "https://glygen.org/publication/PubMed/29796177" } ] }, { "title": "Extracellular gamma-synuclein promotes tumor cell motility by activating beta1 integrin-focal adhesion kinase signaling pathway and increasing matrix metalloproteinase-24, -2 protein secretion.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2018", "authors": "Liu C, Qu L, Zhao C, Shou C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29903032", "url": "https://glygen.org/publication/PubMed/29903032" } ] }, { "title": "Inhibition of epithelial cell migration and Src/FAK signaling by SIRT3.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Lee JJ, van de Ven RAH, Zaganjor E, Ng MR, Barakat A, Demmers JJPG, Finley LWS, Gonzalez Herrera KN, Hung YP, Harris IS, Jeong SM, Danuser G, McAllister SS, Haigis MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029" } ] }, { "title": "Cytotoxic activity of Shp2 inhibitor fumosorinone in human cancer cells.", "journal": "Oncology letters", "date": "2018", "authors": "Chen C, Xue T, Fan P, Meng L, Wei J, Luo D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374" } ] }, { "title": "Simulated Microgravity Reduces Focal Adhesions and Alters Cytoskeleton and Nuclear Positioning Leading to Enhanced Apoptosis via Suppressing FAK/RhoA-Mediated mTORC1/NF-\u03baB and ERK1/2 Pathways.", "journal": "International journal of molecular sciences", "date": "2018-07-08", "authors": "Zhao Tuo, Li Rong, Tan Xin, Zhang Jun, Fan Cuihong, Zhao Qin, Deng Yulin, Xu Aizhang, Lukong Kiven Erique, Genth Harald, Xiang Jim", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29986550", "url": "https://glygen.org/publication/PubMed/29986550" } ] }, { "title": "Inhibition of angiogenesis in endothelial cells by Human Lysyl oxidase propeptide.", "journal": "Scientific reports", "date": "2018", "authors": "Nareshkumar RN, Sulochana KN, Coral K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29993014", "url": "https://glygen.org/publication/PubMed/29993014" } ] }, { "title": "Ulipristal Acetate Interferes With Actin Remodeling Induced by 17beta-Estradiol and Progesterone in Human Endometrial Stromal Cells.", "journal": "Frontiers in endocrinology", "date": "2018", "authors": "Shortrede JE, Montt-Guevara MM, Pennacchio G, Finiguerra M, Giannini A, Genazzani AD, Simoncini T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30013514", "url": "https://glygen.org/publication/PubMed/30013514" } ] }, { "title": "Angiopoietin-like protein 3 blocks nuclear import of FAK and contributes to sorafenib response.", "journal": "British journal of cancer", "date": "2018", "authors": "Bao Y, Yang F, Liu B, Zhao T, Xu Z, Xiong Y, Sun S, Qu L, Wang L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30033448", "url": "https://glygen.org/publication/PubMed/30033448" } ] }, { "title": "Hippo component YAP promotes focal adhesion and tumour aggressiveness via transcriptionally activating THBS1/FAK signalling in breast cancer.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2018-07-28", "authors": "Shen Jie, Cao Beibei, Wang Yatao, Ma Chenshen, Zeng Zhuo, Liu Liang, Li Xiaolan, Tao Deding, Gong Jianping, Xie Daxing", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30055645", "url": "https://glygen.org/publication/PubMed/30055645" } ] }, { "title": "Immune Cell Induced Migration of Osteoprogenitor Cells Is Mediated by TGF-beta Dependent Upregulation of NOX4 and Activation of Focal Adhesion Kinase.", "journal": "International journal of molecular sciences", "date": "2018", "authors": "Ehnert S, Linnemann C, Aspera-Werz RH, Bykova D, Biermann S, Fecht L, De Zwart PM, Nussler AK, Stuby F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30065198", "url": "https://glygen.org/publication/PubMed/30065198" } ] }, { "title": "Knockdown of C1GalT1 inhibits radioresistance of human esophageal cancer cells through modifying beta1-integrin glycosylation.", "journal": "Journal of Cancer", "date": "2018", "authors": "Zhang C, Deng X, Qiu L, Peng F, Geng S, Shen L, Luo Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30087707", "url": "https://glygen.org/publication/PubMed/30087707" } ] }, { "title": "Identification of a novel anoikis signalling pathway using the fungal virulence factor gliotoxin.", "journal": "Nature communications", "date": "2018-08-30", "authors": "Haun Florian, Neumann Simon, Peintner Lukas, Wieland Katrin, Habicht J\u00fcri, Schwan Carsten, \u00d8stevold Kristine, Koczorowska Maria Magdalena, Biniossek Martin, Kist Matthias, Busch Hauke, Boerries Melanie, Davis Roger J, Maurer Ulrich, Schilling Oliver, Aktories Klaus, Borner Christoph", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30166526", "url": "https://glygen.org/publication/PubMed/30166526" } ] }, { "title": "Downregulation of C-Terminal Tensin-Like Protein (CTEN) Suppresses Prostate Cell Proliferation and Contributes to Acinar Morphogenesis.", "journal": "International journal of molecular sciences", "date": "2018-10-16", "authors": "Wu Wei-Ming, Liao Yi-Chun", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30332774", "url": "https://glygen.org/publication/PubMed/30332774" } ] }, { "title": "Knee Extensors Muscle Plasticity Over a 5-Years Rehabilitation Process After Open Knee Surgery.", "journal": "Frontiers in physiology", "date": "2018", "authors": "Fluck M, Viecelli C, Bapst AM, Kasper S, Valdivieso P, Franchi MV, Ruoss S, Luthi JM, Buhler M, Claassen H, Hoppeler H, Gerber C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30337877", "url": "https://glygen.org/publication/PubMed/30337877" } ] }, { "title": "Bivalent Ligand UDCA-LPE Inhibits Pro-Fibrogenic Integrin Signalling by Inducing Lipid Raft-Mediated Internalization.", "journal": "International journal of molecular sciences", "date": "2018", "authors": "Su J, Gan-Schreier H, Goeppert B, Chamulitrat W, Stremmel W, Pathil A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" } ] }, { "title": "Lysyl oxidase-like 2 is a regulator of angiogenesis through modulation of endothelial-to-mesenchymal transition.", "journal": "Journal of cellular physiology", "date": "2019", "authors": "de Jong OG, van der Waals LM, Kools FRW, Verhaar MC, van Balkom BWM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30387148", "url": "https://glygen.org/publication/PubMed/30387148" } ] }, { "title": "Invasion-related circular RNA circFNDC3B inhibits bladder cancer progression through the miR-1178-3p/G3BP2/SRC/FAK axis.", "journal": "Molecular cancer", "date": "2018", "authors": "Liu H, Bi J, Dong W, Yang M, Shi J, Jiang N, Lin T, Huang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30458784", "url": "https://glygen.org/publication/PubMed/30458784" } ] }, { "title": "16-Hydroxycleroda-3,13-dien-15,16-olide induces anoikis in human renal cell carcinoma cells: involvement of focal adhesion disassembly and signaling.", "journal": "OncoTargets and therapy", "date": "2018", "authors": "Chen YC, Huang BM, Lee WC, Chen YC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30464516", "url": "https://glygen.org/publication/PubMed/30464516" } ] }, { "title": "Ski drives an acute increase in MMP-9 gene expression and release in primary cardiac myofibroblasts.", "journal": "Physiological reports", "date": "2018", "authors": "Landry N, Kavosh MS, Filomeno KL, Rattan SG, Czubryt MP, Dixon IMC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30488595", "url": "https://glygen.org/publication/PubMed/30488595" } ] }, { "title": "FAM129B promoted tumor invasion and proliferation via facilitating the phosphorylation of FAK signaling and associated with adverse clinical outcome of non-small cell lung cancer patients.", "journal": "OncoTargets and therapy", "date": "2018", "authors": "Zhou X, Yang F, Zhang Q, Miao Y, Hu X, Li A, Hou G, Wang Q, Kang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362" } ] }, { "title": "Resistance to Src inhibition alters the BRAF-mutant tumor secretome to promote an invasive phenotype and therapeutic escape through a FAK>p130Cas>c-Jun signaling axis.", "journal": "Oncogene", "date": "2019", "authors": "Kessler BE, Mishall KM, Kellett MD, Clark EG, Pugazhenthi U, Pozdeyev N, Kim J, Tan AC, Schweppe RE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30531837", "url": "https://glygen.org/publication/PubMed/30531837" } ] }, { "title": "The FAK inhibitor BI 853520 inhibits spheroid formation and orthotopic tumor growth in malignant pleural mesothelioma.", "journal": "Journal of molecular medicine (Berlin, Germany)", "date": "2019", "authors": "Laszlo V, Valko Z, Ozsvar J, Kovacs I, Garay T, Hoda MA, Klikovits T, Stockhammer P, Aigner C, Groger M, Klepetko W, Berger W, Grusch M, Tovari J, Waizenegger IC, Dome B, Hegedus B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30539198", "url": "https://glygen.org/publication/PubMed/30539198" } ] }, { "title": "Calretinin promotes invasiveness and EMT in malignant mesothelioma cells involving the activation of the FAK signaling pathway.", "journal": "Oncotarget", "date": "2018", "authors": "Worthmuller J, Blum W, Pecze L, Salicio V, Schwaller B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30555628", "url": "https://glygen.org/publication/PubMed/30555628" } ] }, { "title": "Mechanisms of Matrix-Induced Chemoresistance of Breast Cancer Cells-Deciphering Novel Potential Targets for a Cell Sensitization.", "journal": "Cancers", "date": "2018", "authors": "Jakubzig B, Baltes F, Henze S, Schlesinger M, Bendas G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30563275", "url": "https://glygen.org/publication/PubMed/30563275" } ] }, { "title": "Regulation of gastric smooth muscle contraction via Ca2+-dependent and Ca2+-independent actin polymerization.", "journal": "PloS one", "date": "2018", "authors": "Mahavadi S, Nalli AD, Wang H, Kendig DM, Crowe MS, Lyall V, Grider JR, Murthy KS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30571746", "url": "https://glygen.org/publication/PubMed/30571746" } ] }, { "title": "Crabp2 Promotes Metastasis of Lung Cancer Cells via HuR and Integrin beta1/FAK/ERK Signaling.", "journal": "Scientific reports", "date": "2019", "authors": "Wu JI, Lin YP, Tseng CW, Chen HJ, Wang LH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30696915", "url": "https://glygen.org/publication/PubMed/30696915" } ] }, { "title": "The increased adhesion of tumor cells to endothelial cells after irradiation can be reduced by FAK-inhibition.", "journal": "Radiation oncology (London, England)", "date": "2019", "authors": "Nguemgo Kouam P, Buhler H, Hero T, Adamietz IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30717801", "url": "https://glygen.org/publication/PubMed/30717801" } ] }, { "title": "Focal adhesion kinase (FAK) activation by estrogens involves GPER in triple-negative breast cancer cells.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2019", "authors": "Rigiracciolo DC, Santolla MF, Lappano R, Vivacqua A, Cirillo F, Galli GR, Talia M, Muglia L, Pellegrino M, Nohata N, Di Martino MT, Maggiolini M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30728047", "url": "https://glygen.org/publication/PubMed/30728047" } ] }, { "title": "Periostin/\u03b21integrin interaction regulates p21-activated kinases in valvular interstitial cell survival and in actin cytoskeleton reorganization.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2019-05", "authors": "Ghatak Shibnath, Misra Suniti, Moreno-Rodrigue Ricardo A, Hascall Vincent C, Leone Gustavo W, Markwald Roger R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30742951", "url": "https://glygen.org/publication/PubMed/30742951" } ] }, { "title": "Small G protein signalling modulator 2 (SGSM2) is involved in oestrogen receptor-positive breast cancer metastasis through enhancement of migratory cell adhesion via interaction with E-cadherin.", "journal": "Cell adhesion & migration", "date": "2019", "authors": "Lin JH, Lee WJ, Wu HC, Wu CH, Chen LC, Huang CC, Chang HL, Cheng TC, Chang HW, Ho CT, Tu SH, Ho YS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30744493", "url": "https://glygen.org/publication/PubMed/30744493" } ] }, { "title": "Inhibition of FAK Signaling Elicits Lamin A/C-Associated Nuclear Deformity and Cellular Senescence.", "journal": "Frontiers in oncology", "date": "2019", "authors": "Chuang Hsiang-Hao, Wang Pei-Hui, Niu Sheng-Wen, Zhen Yen-Yi, Huang Ming-Shyan, Hsiao Michael, Yang Chih-Jen", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269" } ] }, { "title": "The knocking down of the oncoprotein Golgi phosphoprotein 3 in T98G cells of glioblastoma multiforme disrupts cell migration by affecting focal adhesion dynamics in a focal adhesion kinase-dependent manner.", "journal": "PloS one", "date": "2019", "authors": "Arriagada C, Luchsinger C, Gonzalez AE, Schwenke T, Arriagada G, Folch H, Ehrenfeld P, Burgos PV, Mardones GA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30779783", "url": "https://glygen.org/publication/PubMed/30779783" } ] }, { "title": "Repulsive guidance molecule a suppresses seizures and mossy fiber sprouting via the FAKp120RasGAPRas signaling pathway.", "journal": "Molecular medicine reports", "date": "2019", "authors": "Song M, Tian F, Xia H, Xie Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30816469", "url": "https://glygen.org/publication/PubMed/30816469" } ] }, { "title": "Glucose Drives Growth Factor-Independent Esophageal Cancer Proliferation via Phosphohistidine-Focal Adhesion Kinase Signaling.", "journal": "Cellular and molecular gastroenterology and hepatology", "date": "2019", "authors": "Zhang J, Gelman IH, Katsuta E, Liang Y, Wang X, Li J, Qu J, Yan L, Takabe K, Hochwald SN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30836148", "url": "https://glygen.org/publication/PubMed/30836148" } ] }, { "title": "Phosphorylation Regulates CAP1 (Cyclase-Associated Protein 1) Functions in the Motility and Invasion of Pancreatic Cancer Cells.", "journal": "Scientific reports", "date": "2019", "authors": "Wu H, Hasan R, Zhang H, Gray J, Williams D, Miller M, Allen F, Lee V, Kelly T, Zhou GL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30894654", "url": "https://glygen.org/publication/PubMed/30894654" } ] }, { "title": "Exploration of Dynamic Elastic Modulus Changes on Glioblastoma Cell Populations with Aberrant EGFR Expression as a Potential Therapeutic Intervention Using a Tunable Hyaluronic Acid Hydrogel Platform.", "journal": "Gels (Basel, Switzerland)", "date": "2017-07-13", "authors": "Sivakumar Hemamylammal, Strowd Roy, Skardal Aleksander", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30920523", "url": "https://glygen.org/publication/PubMed/30920523" } ] }, { "title": "Focal adhesion kinase (FAK) phosphorylation is a key regulator of embryonal rhabdomyosarcoma (ERMS) cell viability and migration.", "journal": "Journal of cancer research and clinical oncology", "date": "2019", "authors": "Al-Ghabkari A, Qasrawi DO, Alshehri M, Narendran A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845" } ] }, { "title": "Neuropilin-1 aggravates liver cirrhosis by promoting angiogenesis via VEGFR2-dependent PI3K/Akt pathway in hepatic sinusoidal endothelial cells.", "journal": "EBioMedicine", "date": "2019", "authors": "Wang L, Feng Y, Xie X, Wu H, Su XN, Qi J, Xin W, Gao L, Zhang Y, Shah VH, Zhu Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31060904", "url": "https://glygen.org/publication/PubMed/31060904" } ] }, { "title": "EPHB6 mutation induces cell adhesion-mediated paclitaxel resistance via EPHA2 and CDH11 expression.", "journal": "Experimental & molecular medicine", "date": "2019", "authors": "Yoon S, Choi JH, Kim SJ, Lee EJ, Shah M, Choi S, Woo HG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31160603", "url": "https://glygen.org/publication/PubMed/31160603" } ] }, { "title": "Apigenin inhibits growth and migration of fibroblasts by suppressing FAK signaling.", "journal": "Aging", "date": "2019", "authors": "Wang H, Guo B, Lin S, Chang P, Tao K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31170089", "url": "https://glygen.org/publication/PubMed/31170089" } ] }, { "title": "ZINC4085554 inhibits cancer cell adhesion by interfering with the interaction of Akt1 and FAK.", "journal": "Oncology letters", "date": "2019", "authors": "More SK, Vomhof-Dekrey EE, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31186741", "url": "https://glygen.org/publication/PubMed/31186741" } ] }, { "title": "Depletion of Host Cell Focal Adhesion Kinase Increases the Susceptibility to Invasion by Trypanosoma cruzi Metacyclic Forms.", "journal": "Frontiers in cellular and infection microbiology", "date": "2019", "authors": "Onofre Thiago Souza, Rodrigues Jo\u00e3o Paulo Ferreira, Yoshida Nobuko", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31297342", "url": "https://glygen.org/publication/PubMed/31297342" } ] }, { "title": "Niclosamide reverses adipocyte induced epithelial-mesenchymal transition in breast cancer cells via suppression of the interleukin-6/STAT3 signalling axis.", "journal": "Scientific reports", "date": "2019", "authors": "Gyamfi J, Lee YH, Min BS, Choi J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31383893", "url": "https://glygen.org/publication/PubMed/31383893" } ] }, { "title": "N-glycosylation-defective splice variants of neuropilin-1 promote metastasis by activating endosomal signals.", "journal": "Nature communications", "date": "2019-08-16", "authors": "Huang Xiuping, Ye Qing, Chen Min, Li Aimin, Mi Wenting, Fang Yuxin, Zaytseva Yekaterina Y, O'Connor Kathleen L, Vander Kooi Craig W, Liu Side, She Qing-Bai", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31420553", "url": "https://glygen.org/publication/PubMed/31420553" } ] }, { "title": "Atezolizumab potentiates Tcell-mediated cytotoxicity and coordinates with FAK to suppress cell invasion and motility in PD-L1+ triple negative breast cancer cells.", "journal": "Oncoimmunology", "date": "2019", "authors": "Mohan Nishant, Hosain Salman, Zhao Jun, Shen Yi, Luo Xiao, Jiang Jiangsong, Endo Yukinori, Wu Wen Jin", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31428520", "url": "https://glygen.org/publication/PubMed/31428520" } ] }, { "title": "FAK activity sustains intrinsic and acquired ovarian cancer resistance to platinum chemotherapy.", "journal": "eLife", "date": "2019-09-03", "authors": "Diaz Osterman Carlos J, Ozmadenci Duygu, Kleinschmidt Elizabeth G, Taylor Kristin N, Barrie Allison M, Jiang Shulin, Bean Lisa M, Sulzmaier Florian J, Jean Christine, Tancioni Isabelle, Anderson Kristen, Uryu Sean, Cordasco Edward A, Li Jian, Chen Xiao Lei, Fu Guo, Ojalill Marjaana, Rappu Pekka, Heino Jyrki, Mark Adam M, Xu Guorong, Fisch Kathleen M, Kolev Vihren N, Weaver David T, Pachter Jonathan A, Gy\u0151rffy Bal\u00e1zs, McHale Michael T, Connolly Denise C, Molinolo Alfredo, Stupack Dwayne G, Schlaepfer David D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31478830", "url": "https://glygen.org/publication/PubMed/31478830" } ] }, { "title": "FAK-Copy-Gain Is a Predictive Marker for Sensitivity to FAK Inhibition in Breast Cancer.", "journal": "Cancers", "date": "2019-09-02", "authors": "Kim Young-Ho, Kim Hyun-Kyoung, Kim Hee Yeon, Gawk HyeRan, Bae Seung-Hyun, Sim Hye Won, Kang Eun-Kyung, Seoh Ju-Young, Jang Hyonchol, Hong Kyeong-Man", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31480645", "url": "https://glygen.org/publication/PubMed/31480645" } ] }, { "title": "Identification of new binding proteins of focal adhesion kinase using immunoprecipitation and mass spectrometry.", "journal": "Scientific reports", "date": "2019-09-09", "authors": "Nguyen Binh Thanh, Pyun Jae-Chul, Lee Sang-Guk, Kang Min-Jung", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31501460", "url": "https://glygen.org/publication/PubMed/31501460" } ] }, { "title": "Cytosolic phospholipase A2\u03b1 modulates cell-matrix adhesion via the FAK/paxillin pathway in hepatocellular carcinoma.", "journal": "Cancer biology & medicine", "date": "2019-05", "authors": "Guo Piao, He Yuchao, Chen Lu, Qi Lisha, Liu Dongming, Chen Ziye, Xiao Manyu, Chen Liwei, Luo Yi, Zhang Ning, Guo Hua", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31516757", "url": "https://glygen.org/publication/PubMed/31516757" } ] }, { "title": "Focal Adhesion Kinase Inhibition Contributes to Tumor Cell Survival and Motility in Neuroblastoma Patient-Derived Xenografts.", "journal": "Scientific reports", "date": "2019-09-13", "authors": "Stafman Laura L, Williams Adele P, Marayati Raoud, Aye Jamie M, Markert Hooper R, Garner Evan F, Quinn Colin H, Lallani Shoeb B, Stewart Jerry E, Yoon Karina J, Whelan Kimberly, Beierle Elizabeth A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31519958", "url": "https://glygen.org/publication/PubMed/31519958" } ] }, { "title": "Leptin Promotes Expression of EMT-Related Transcription Factors and Invasion in a Src and FAK-Dependent Pathway in MCF10A Mammary Epithelial Cells.", "journal": "Cells", "date": "2019-09-24", "authors": "Olea-Flores Monserrat, Zu\u00f1iga-Eulogio Miriam, Tacuba-Saavedra Arvey, Bueno-Salgado Magdalena, S\u00e1nchez-Carvajal Andrea, Vargas-Santiago Yovani, Mendoza-Catal\u00e1n Miguel A, P\u00e9rez Salazar Eduardo, Garc\u00eda-Hern\u00e1ndez Alejandra, Padilla-Benavides Teresita, Navarro-Tito Napole\u00f3n", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31554180", "url": "https://glygen.org/publication/PubMed/31554180" } ] }, { "title": "The effects of focal adhesion kinase and platelet-derived growth factor receptor beta inhibition in a patient-derived xenograft model of primary and metastatic Wilms tumor.", "journal": "Oncotarget", "date": "2019-09-17", "authors": "Aye Jamie M, Stafman Laura L, Williams Adele P, Garner Evan F, Stewart Jerry E, Anderson Joshua C, Mruthyunjayappa Smitha, Waldrop Mary G, Goolsby Caroline D, Markert Hooper R, Quinn Colin, Marayati Raoud, Mroczek-Musulman Elizabeth, Willey Christopher D, Yoon Karina J, Whelan Kimberly F, Beierle Elizabeth A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31565187", "url": "https://glygen.org/publication/PubMed/31565187" } ] }, { "title": "12N-Substituted Matrinol Derivatives Inhibited the Expression of Fibrogenic Genes via Repressing Integrin/FAK/PI3K/Akt Pathway in Hepatic Stellate Cells.", "journal": "Molecules (Basel, Switzerland)", "date": "2019-10-17", "authors": "Bao Yunyang, Pang Yudong, Tang Sheng, Niu Tianyun, Guo Zhihao, He Hongwei, Li Yinghong, Song Danqing", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31627430", "url": "https://glygen.org/publication/PubMed/31627430" } ] }, { "title": "Circular RNA circPICALM sponges miR-1265 to inhibit bladder cancer metastasis and influence FAK phosphorylation.", "journal": "EBioMedicine", "date": "2019", "authors": "Yan D, Dong W, He Q, Yang M, Huang L, Kong J, Qin H, Lin T, Huang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31648990", "url": "https://glygen.org/publication/PubMed/31648990" } ] }, { "title": "Adenylyl Cyclase Type 8 Overexpression Impairs Phosphorylation-Dependent Orai1 Inactivation and Promotes Migration in MDA-MB-231 Breast Cancer Cells.", "journal": "Cancers", "date": "2019-10-23", "authors": "Sanchez-Collado Jose, Lopez Jose J, Jardin Isaac, Camello Pedro J, Falcon Debora, Regodon Sergio, Salido Gines M, Smani Tarik, Rosado Juan A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31652779", "url": "https://glygen.org/publication/PubMed/31652779" } ] }, { "title": "Accumulation of tissue factor in endothelial cells promotes cellular apoptosis through over-activation of Src1 and involves \u03b21-integrin signalling.", "journal": "Apoptosis : an international journal on programmed cell death", "date": "2020-02", "authors": "Ethaeb Ali M, Mohammad Mohammad A, Madkhali Yahya, Featherby Sophie, Maraveyas Anthony, Greenman John, Ettelaie Camille", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31654241", "url": "https://glygen.org/publication/PubMed/31654241" } ] }, { "title": "Leptin induces cell migration and invasion in a FAK-Src-dependent manner in breast cancer cells.", "journal": "Endocrine connections", "date": "2019-11", "authors": "Ju\u00e1rez-Cruz Juan Carlos, Zu\u00f1iga-Eulogio Miriam Daniela, Olea-Flores Monserrat, Casta\u00f1eda-Saucedo Eduardo, Mendoza-Catal\u00e1n Miguel \u00c1ngel, Ortu\u00f1o-Pineda Carlos, Moreno-God\u00ednez Ma Elena, Villegas-Comonfort S\u00f3crates, Padilla-Benavides Teresita, Navarro-Tito Napole\u00f3n", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408" } ] }, { "title": "Modulation of Calretinin Expression in Human Mesothelioma Cells Reveals the Implication of the FAK and Wnt Signaling Pathways in Conferring Chemoresistance towards Cisplatin.", "journal": "International journal of molecular sciences", "date": "2019-10-29", "authors": "W\u00f6rthm\u00fcller Janine, Salicio Val\u00e9rie, Oberson Anne, Blum Walter, Schwaller Beat", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31671889", "url": "https://glygen.org/publication/PubMed/31671889" } ] }, { "title": "Dietary delphinidin inhibits human colorectal cancer metastasis associating with upregulation of miR-204-3p and suppression of the integrin/FAK axis.", "journal": "Scientific reports", "date": "2019-12-12", "authors": "Huang Chi-Chou, Hung Chia-Hung, Hung Tung-Wei, Lin Yi-Chieh, Wang Chau-Jong, Kao Shao-Hsuan", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31831830", "url": "https://glygen.org/publication/PubMed/31831830" } ] }, { "title": "PEP06 polypeptide 30 is a novel cluster-dissociating agent inhibiting v integrin/FAK/Src signaling in oral squamous cell carcinoma cells.", "journal": "Acta pharmaceutica Sinica. B", "date": "2019-11", "authors": "Tuguzbaeva Gulnara, Yue Er, Chen Xi, He Lina, Li Xinlei, Ju Jiaming, Qin Ying, Pavlov Valentin, Lu Yanjie, Jia Wenting, Bai Yunlong, Niu Yumei, Yang Baofeng", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31867162", "url": "https://glygen.org/publication/PubMed/31867162" } ] }, { "title": "Metformin Inhibit Cervical Cancer Migration by Suppressing the FAK/Akt Signaling Pathway.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "date": "2019-12-01", "authors": "Hakimee Henna, Hutamekalin Pilaiwanwadee, Tanasawet Supita, Chonpathompikunlert Pennapa, Tipmanee Varomyalin, Sukketsiri Wanida", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31870092", "url": "https://glygen.org/publication/PubMed/31870092" } ] }, { "title": "Glutathione peroxidase-1 regulates adhesion and metastasis of triple-negative breast cancer cells via FAK signaling.", "journal": "Redox biology", "date": "2020-01", "authors": "Lee Eunkyung, Choi Ahyoung, Jun Yukyung, Kim Namhee, Yook Jong In, Kim Soo Youl, Lee Sanghyuk, Kang Sang Won", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31926619", "url": "https://glygen.org/publication/PubMed/31926619" } ] }, { "title": "FAK Deficiency in Bone Marrow Stromal Cells Alters Their Homeostasis and Drives Abnormal Proliferation and Differentiation of Haematopoietic Stem Cells.", "journal": "Cells", "date": "2020-03-06", "authors": "Wu Yuenv, Campos Lydia, Daguenet Elisabeth, He Zhiguo, Picot Tiphanie, Tavernier-Tardy Emmanuelle, Soglu Gilbert, Guyotat Denis, Aanei Carmen-Mariana", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32155953", "url": "https://glygen.org/publication/PubMed/32155953" } ] }, { "title": "Luteolin attenuates migration and invasion of lung cancer cells via suppressing focal adhesion kinase and non-receptor tyrosine kinase signaling pathway.", "journal": "Nutrition research and practice", "date": "2020-04", "authors": "Masraksa Wuttipong, Tanasawet Supita, Hutamekalin Pilaiwanwadee, Wongtawatchai Tulaporn, Sukketsiri Wanida", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32256987", "url": "https://glygen.org/publication/PubMed/32256987" } ] }, { "title": "Raftlin is recruited by neuropilin-1 to the activated VEGFR2 complex to control proangiogenic signaling.", "journal": "Angiogenesis", "date": "2020", "authors": "Bayliss AL, Sundararaman A, Granet C, Mellor H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611" } ] }, { "title": "MOB2 suppresses GBM cell migration and invasion via regulation of FAK/Akt and cAMP/PKA signaling.", "journal": "Cell death & disease", "date": "2020", "authors": "Jiang K, Yao G, Hu L, Yan Y, Liu J, Shi J, Chang Y, Zhang Y, Liang D, Shen D, Zhang G, Meng S, Piao H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32286266", "url": "https://glygen.org/publication/PubMed/32286266" } ] }, { "title": "EPH receptor B2 stimulates human monocyte adhesion and migration independently of its EphrinB ligands.", "journal": "Journal of leukocyte biology", "date": "2020", "authors": "Vreeken D, Bruikman CS, Cox SML, Zhang H, Lalai R, Koudijs A, van Zonneveld AJ, Hovingh GK, van Gils JM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32337793", "url": "https://glygen.org/publication/PubMed/32337793" } ] }, { "title": "Targeting lysyl oxidase (LOX) overcomes chemotherapy resistance in triple negative breast cancer.", "journal": "Nature communications", "date": "2020-05-15", "authors": "Saatci Ozge, Kaymak Aysegul, Raza Umar, Ersan Pelin G, Akbulut Ozge, Banister Carolyn E, Sikirzhytski Vitali, Tokat Unal Metin, Aykut Gamze, Ansari Suhail A, Dogan Hayriye Tatli, Dogan Mehmet, Jandaghi Pouria, Isik Aynur, Gundogdu Fatma, Kosemehmetoglu Kemal, Dizdar Omer, Aksoy Sercan, Akyol Aytekin, Uner Aysegul, Buckhaults Phillip J, Riazalhosseini Yasser, Sahin Ozgur", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32415208", "url": "https://glygen.org/publication/PubMed/32415208" } ] }, { "title": "Redox Regulation of NOX Isoforms on FAK(Y397)/SRC(Y416) Phosphorylation Driven Epithelial-to-Mesenchymal Transition in Malignant Cervical Epithelial Cells.", "journal": "Cells", "date": "2020-06-26", "authors": "Kim Young Mee, Muthuramalingam Karthika, Cho Moonjae", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32604782", "url": "https://glygen.org/publication/PubMed/32604782" } ] }, { "title": "Controlling Fibronectin Fibrillogenesis Using Visible Light.", "journal": "Frontiers in molecular biosciences", "date": "2020", "authors": "Gudzenko Tetyana, Franz Clemens M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32733919", "url": "https://glygen.org/publication/PubMed/32733919" } ] }, { "title": "Design, synthesis and biological evaluation of ring-fused pyrazoloamino pyridine/pyrimidine derivatives as potential FAK inhibitors.", "journal": "Bioorganic & medicinal chemistry letters", "date": "2020-11-01", "authors": "Xie Hongming, Lin Xinglong, Zhang Yingjun, Tan Fuxing, Chi Bo, Peng Zhihong, Dong Wanrong, An Delie", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32784087", "url": "https://glygen.org/publication/PubMed/32784087" } ] }, { "title": "Focal Adhesion Kinase (FAK) Over-Expression and Prognostic Implication in Pediatric Hepatocellular Carcinoma.", "journal": "International journal of molecular sciences", "date": "2020-08-12", "authors": "Francalanci Paola, Giovannoni Isabella, De Stefanis Cristiano, Romito Ilaria, Grimaldi Chiara, Castellano Aurora, D'Oria Valentina, Alaggio Rita, Alisi Anna", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32806748", "url": "https://glygen.org/publication/PubMed/32806748" } ] }, { "title": "Pleckstrin homology domain of phospholipase D2 is a negative regulator of focal adhesion kinase.", "journal": "BMB reports", "date": "2021-02", "authors": "Kim Mi Kyoung, Hwang Won Chan, Min Do Sik", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" } ] }, { "title": "Arginine methylation of SHANK2 by PRMT7 promotes human breast cancer metastasis through activating endosomal FAK signalling.", "journal": "eLife", "date": "2020-08-26", "authors": "Liu Yingqi, Li Lingling, Liu Xiaoqing, Wang Yibo, Liu Lingxia, Peng Lu, Liu Jiayuan, Zhang Lian, Wang Guannan, Li Hongyuan, Liu Dong-Xu, Huang Baiqu, Lu Jun, Zhang Yu", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32844749", "url": "https://glygen.org/publication/PubMed/32844749" } ] }, { "title": "ITGB3-mediated uptake of small extracellular vesicles facilitates intercellular communication in breast cancer cells.", "journal": "Nature communications", "date": "2020", "authors": "Fuentes P, Sese M, Guijarro PJ, Emperador M, Sanchez-Redondo S, Peinado H, Hummer S, Ramon Y Cajal S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32848136", "url": "https://glygen.org/publication/PubMed/32848136" } ] }, { "title": "Loss of the Essential Autophagy Regulators FIP200 or Atg5 Leads to Distinct Effects on Focal Adhesion Composition and Organization.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Assar Emelia A, Tumbarello David A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32850845", "url": "https://glygen.org/publication/PubMed/32850845" } ] }, { "title": "Synergistic Interactions of 5-Fluorouracil with Inhibitors of Protein Kinase CK2 Correlate with p38 MAPK Activation and FAK Inhibition in the Triple-Negative Breast Cancer Cell Line.", "journal": "International journal of molecular sciences", "date": "2020-08-28", "authors": "Wi\u0144ska Patrycja, Karatsai Olena, Staniszewska Monika, Koronkiewicz Miros\u0142awa, Chojnacki Konrad, R\u0119dowicz Maria Jolanta", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32872257", "url": "https://glygen.org/publication/PubMed/32872257" } ] }, { "title": "FAK activity in cancer-associated fibroblasts is a prognostic marker and a druggable key metastatic player in pancreatic cancer.", "journal": "EMBO molecular medicine", "date": "2020-11-06", "authors": "Zaghdoudi Sonia, Decaup Emilie, Belhabib Ismahane, Samain R\u00e9mi, Cassant-Sourdy St\u00e9phanie, Rochotte Julia, Brunel Alexia, Schlaepfer David, Cros J\u00e9rome, Neuzillet Cindy, Strehaiano Manon, Alard Amandine, Tomasini Richard, Rajeeve Vinothini, Perraud Aur\u00e9lie, Mathonnet Muriel, Pearce Oliver Mt, Martineau Yvan, Pyronnet St\u00e9phane, Bousquet Corinne, Jean Christine", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33025708", "url": "https://glygen.org/publication/PubMed/33025708" } ] }, { "title": "Long-Term Low-Dose Delta-9-Tetrahydrocannbinol (THC) Administration to Simian Immunodeficiency Virus (SIV) Infected Rhesus Macaques Stimulates the Release of Bioactive Blood Extracellular Vesicles (EVs) that Induce Divergent Structural Adaptations and Signaling Cues.", "journal": "Cells", "date": "2020-10-06", "authors": "Lyu Yuan, Kopcho Steven, Mohan Mahesh, Okeoma Chioma M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33036231", "url": "https://glygen.org/publication/PubMed/33036231" } ] }, { "title": "Carbohydrate-Induced Insulin Signaling Activates Focal Adhesion Kinase: A Nutrient and Mechanotransduction Crossroads.", "journal": "Nutrients", "date": "2020-10-15", "authors": "Wilburn Dylan T, Machek Steven B, Cardaci Thomas D, Willoughby Darryn S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33076263", "url": "https://glygen.org/publication/PubMed/33076263" } ] }, { "title": "Exosome-derived ENO1 regulates integrin \u03b16\u03b24 expression and promotes hepatocellular carcinoma growth and metastasis.", "journal": "Cell death & disease", "date": "2020-11-12", "authors": "Jiang Keqiu, Dong Chengyong, Yin Zeli, Li Rui, Mao Jiakai, Wang Chengye, Zhang Junlin, Gao Zhenming, Liang Rui, Wang Qi, Wang Liming", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263" } ] }, { "title": "Abnormally activated OPN/integrin \u03b1V\u03b23/FAK signalling is responsible for EGFR-TKI resistance in EGFR mutant non-small-cell lung cancer.", "journal": "Journal of hematology & oncology", "date": "2020-12-07", "authors": "Fu Yulong, Zhang Yang, Lei Zhe, Liu Ting, Cai Tingting, Wang Anqi, Du Wenwen, Zeng Yuanyuan, Zhu Jianjie, Liu Zeyi, Huang Jian-An", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33287873", "url": "https://glygen.org/publication/PubMed/33287873" } ] }, { "title": "FAK displacement from focal adhesions: a promising strategy to target processes implicated in cancer progression and metastasis.", "journal": "Cell communication and signaling : CCS", "date": "2021-01-07", "authors": "Antoniades Ioanna, Kyriakou Maria, Charalambous Anna, Kalalidou Katerina, Christodoulou Andri, Christoforou Maria, Skourides Paris A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438" } ] }, { "title": "C1GALT1 high expression is associated with poor survival of patients with pancreatic ductal adenocarcinoma and promotes cell invasiveness through integrin alphav.", "journal": "Oncogene", "date": "2021", "authors": "Kuo TC, Wu MH, Yang SH, Chen ST, Hsu TW, Jhuang JY, Liao YY, Tien YW, Huang MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33420364", "url": "https://glygen.org/publication/PubMed/33420364" } ] }, { "title": "Chrysin serves as a novel inhibitor of DGK\u03b1/FAK interaction to suppress the malignancy of esophageal squamous cell carcinoma (ESCC).", "journal": "Acta pharmaceutica Sinica. B", "date": "2021-01", "authors": "Chen Jie, Wang Yan, Zhao Di, Zhang Lingyuan, Zhang Weimin, Fan Jiawen, Li Jinting, Zhan Qimin", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33532186", "url": "https://glygen.org/publication/PubMed/33532186" } ] }, { "title": "Molecular Basis of LH Action on Breast Cancer Cell Migration and Invasion via Kinase and Scaffold Proteins.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Mondaca Joselina Magali, Uzair Ivonne Denise, Castro Guijarro Ana Carla, Flamini Marina In\u00e9s, Sanchez Angel Matias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" } ] }, { "title": "Carbon Ion Irradiation Enhances the Anti-tumor Efficiency in Tongue Squamous Cell Carcinoma via Modulating the FAK Signaling.", "journal": "Frontiers in public health", "date": "2021", "authors": "Si Qingzong, Ye Qian, Bing Zhitong, Fan Ruihong, Hu Xiaoli, Liu Bin, Wang Jizeng, Liu Yang, An Xiaoli", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33634070", "url": "https://glygen.org/publication/PubMed/33634070" } ] }, { "title": "EB1 Restricts Breast Cancer Cell Invadopodia Formation and Matrix Proteolysis via FAK.", "journal": "Cells", "date": "2021", "authors": "Chanez B, Ostacolo K, Badache A, Thuault S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33668531", "url": "https://glygen.org/publication/PubMed/33668531" } ] }, { "title": "ZINC40099027 activates human focal adhesion kinase by accelerating the enzymatic activity of the FAK kinase domain.", "journal": "Pharmacology research & perspectives", "date": "2021-04", "authors": "Rashmi , More Shyam K, Wang Qinggang, Vomhof-DeKrey Emilie E, Porter James E, Basson Marc D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33715263", "url": "https://glygen.org/publication/PubMed/33715263" } ] }, { "title": "The Netrin-1-Neogenin-1 signaling axis controls neuroblastoma cell migration via integrin-\u03b21 and focal adhesion kinase activation.", "journal": "Cell adhesion & migration", "date": "2021-12", "authors": "Villanueva Andrea A, Sanchez-Gomez Pilar, Mu\u00f1oz-Palma Ernesto, Puvogel Sof\u00eda, Casas B\u00e1rbara S, Arriagada Cecilia, Pe\u00f1a-Villalobos Isaac, Lois Pablo, Ram\u00edrez Orellana Manuel, Lubieniecki Fabiana, Casco Claro Fernando, Gallegos Iv\u00e1n, Garc\u00eda-Castro Javier, Torres Vicente A, Palma Ver\u00f3nica", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33724150", "url": "https://glygen.org/publication/PubMed/33724150" } ] }, { "title": "Focal adhesion kinase inhibition synergizes with nab-paclitaxel to target pancreatic ductal adenocarcinoma.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2021-03-09", "authors": "Le Large T Y S, Bijlsma M F, El Hassouni B, Mantini G, Lagerweij T, Henneman A A, Funel N, Kok B, Pham T V, de Haas R, Morelli L, Knol J C, Piersma S R, Kazemier G, van Laarhoven H W M, Giovannetti E, Jimenez C R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33750427", "url": "https://glygen.org/publication/PubMed/33750427" } ] }, { "title": "Potential Antimetastatic Effect of Timosaponin AIII against Human Osteosarcoma Cells through Regulating the Integrin/FAK/Cofilin Axis.", "journal": "Pharmaceuticals (Basel, Switzerland)", "date": "2021-03-14", "authors": "Hsieh Yi-Hsien, Hsu Wen-Hung, Yang Shun-Fa, Liu Chung-Jung, Lu Ko-Hsiu, Wang Pei-Han, Lin Renn-Chia", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33799345", "url": "https://glygen.org/publication/PubMed/33799345" } ] }, { "title": "Inhibitory effects of terrein on lung cancer cell metastasis and angiogenesis.", "journal": "Oncology reports", "date": "2021-06", "authors": "Buachan Paiwan, Namsa-Aid Maneekarn, Sung Hye Kyoung, Peng Chun, Sweeney Gary, Tanechpongtamb Wanlaya", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33846818", "url": "https://glygen.org/publication/PubMed/33846818" } ] }, { "title": "Maintenance of HDACs and H3K9me3 Prevents Arterial Flow-Induced Venous Endothelial Damage.", "journal": "Frontiers in cell and developmental biology", "date": "2021", "authors": "Wang Ting-Yun, Chang Ming-Min, Li Yi-Shuan Julie, Huang Tzu-Chieh, Chien Shu, Wu Chia-Ching", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33898431", "url": "https://glygen.org/publication/PubMed/33898431" } ] }, { "title": "hTERT Downregulation Attenuates Resistance to DOX, Impairs FAK-Mediated Adhesion, and Leads to Autophagy Induction in Breast Cancer Cells.", "journal": "Cells", "date": "2021-04-10", "authors": "Romaniuk-Drapa\u0142a Aleksandra, Toto\u0144 Ewa, Konieczna Natalia, Machnik Marta, Barczak Wojciech, Kowal Dagmar, Kopczy\u0144ski Przemys\u0142aw, Kaczmarek Mariusz, Rubi\u015b B\u0142a\u017cej", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284" } ] }, { "title": "The extracellular-regulated protein kinase 5 (ERK5) enhances metastatic burden in triple-negative breast cancer through focal adhesion protein kinase (FAK)-mediated regulation of cell adhesion.", "journal": "Oncogene", "date": "2021-06", "authors": "Xu Qiuping, Zhang Jingwei, Telfer Brian A, Zhang Hao, Ali Nisha, Chen Fuhui, Risa Blanca, Pearson Adam J, Zhang Wei, Finegan Katherine G, Ucar Ahmet, Giurisato Emanuele, Tournier Cathy", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33981002", "url": "https://glygen.org/publication/PubMed/33981002" } ] }, { "title": "Focal adhesion kinase inhibitor BI 853520 inhibits cell proliferation, migration and EMT process through PI3K/AKT/mTOR signaling pathway in ovarian cancer.", "journal": "Discover. Oncology", "date": "2021-08-30", "authors": "Li Hong, Gao Yizhi, Ren Chenchen", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35201437", "url": "https://glygen.org/publication/PubMed/35201437" } ] }, { "title": "MCPIP1 regulates focal adhesion kinase and Rho GTPase-dependent migration in clear cell renal cell carcinoma.", "journal": "European journal of pharmacology", "date": "2022", "authors": "Gorka J, Marona P, Kwapisz O, Rys J, Jura J, Miekus K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35257717", "url": "https://glygen.org/publication/PubMed/35257717" } ] }, { "title": "ATX/LPA axis regulates FAK activation, cell proliferation, apoptosis, and motility in human pancreatic cancer cells.", "journal": "In vitro cellular & developmental biology. Animal", "date": "2022-04", "authors": "Liao Yan, Liu Lei, Yang Jiayao, Shi Zhaohong", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35426066", "url": "https://glygen.org/publication/PubMed/35426066" } ] }, { "title": "Tumor-associated macrophage (TAM)-derived CCL22 induces FAK addiction in esophageal squamous cell carcinoma (ESCC).", "journal": "Cellular & molecular immunology", "date": "2022", "authors": "Chen J, Zhao D, Zhang L, Zhang J, Xiao Y, Wu Q, Wang Y, Zhan Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35962191", "url": "https://glygen.org/publication/PubMed/35962191" } ] }, { "title": "RIOK3 promotes pancreatic ductal adenocarcinoma cell invasion and metastasis by stabilizing FAK.", "journal": "Heliyon", "date": "2022-08", "authors": "Xu Mengyuan, Fang Lei, Guo Xin, Qin Henan, Sun Rui, Ning Zhen, Wang Aman", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35982848", "url": "https://glygen.org/publication/PubMed/35982848" } ] }, { "title": "Increased Stiffness Downregulates Focal Adhesion Kinase Expression in Pancreatic Cancer Cells Cultured in 3D Self-Assembling Peptide Scaffolds.", "journal": "Biomedicines", "date": "2022-07-29", "authors": "Betriu Nausika, Andreeva Anna, Alonso Anna, Semino Carlos E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "36009384", "url": "https://glygen.org/publication/PubMed/36009384" } ] }, { "title": "Convergent signalling in the action of integrins, neuropeptides, growth factors and oncogenes.", "journal": "Cancer surveys", "date": "1995", "authors": "Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "7553664", "url": "https://glygen.org/publication/PubMed/7553664" } ] }, { "title": "Identification of Tyr-397 as the primary site of tyrosine phosphorylation and pp60src association in the focal adhesion kinase, pp125FAK.", "journal": "Molecular and cellular biology", "date": "1995-05", "authors": "Eide B L, Turck C W, Escobedo J A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "7739563", "url": "https://glygen.org/publication/PubMed/7739563" } ] }, { "title": "A transmembrane-anchored chimeric focal adhesion kinase is constitutively activated and phosphorylated at tyrosine residues identical to pp125FAK.", "journal": "The Journal of biological chemistry", "date": "1994-08-12", "authors": "Chan P Y, Kanner S B, Whitney G, Aruffo A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "8051157", "url": "https://glygen.org/publication/PubMed/8051157" } ] }, { "title": "Phosphorylation of tyrosine 397 in focal adhesion kinase is required for binding phosphatidylinositol 3-kinase.", "journal": "The Journal of biological chemistry", "date": "1996", "authors": "Chen HC, Appeddu PA, Isoda H, Guan JL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "8824286", "url": "https://glygen.org/publication/PubMed/8824286" } ] }, { "title": "Focal adhesion kinase tyrosine-861 is a major site of phosphorylation by Src.", "journal": "Biochemical and biophysical research communications", "date": "1996", "authors": "Calalb MB, Zhang X, Polte TR, Hanks SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336" } ] }, { "title": "Focal adhesion kinase overexpression enhances ras-dependent integrin signaling to ERK2/mitogen-activated protein kinase through interactions with and activation of c-Src.", "journal": "The Journal of biological chemistry", "date": "1997", "authors": "Schlaepfer DD, Hunter T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9148935", "url": "https://glygen.org/publication/PubMed/9148935" } ] }, { "title": "Role of focal adhesion kinase in integrin signaling.", "journal": "The international journal of biochemistry & cell biology", "date": "1997", "authors": "Guan J L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9416004", "url": "https://glygen.org/publication/PubMed/9416004" } ] }, { "title": "Dissociation of FAK/p130(CAS)/c-Src complex during mitosis: role of mitosis-specific serine phosphorylation of FAK.", "journal": "The Journal of cell biology", "date": "1999-01-25", "authors": "Yamakita Y, Totsukawa G, Yamashiro S, Fry D, Zhang X, Hanks S K, Matsumura F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9922457", "url": "https://glygen.org/publication/PubMed/9922457" } ] }, { "title": "The proto-oncogene Fgr regulates cell migration and this requires its plasma membrane localization.", "journal": "Experimental cell research", "date": "2005", "authors": "Continolo S, Baruzzi A, Majeed M, Caveggion E, Fumagalli L, Lowell CA, Berton G", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106" } ] }, { "title": "Specific tyrosine phosphorylation of focal adhesion kinase mediated by Fer tyrosine kinase in suspended hepatocytes.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Oh MA, Choi S, Lee MJ, Choi MC, Lee SA, Ko W, Cance WG, Oh ES, Buday L, Kim SH, Lee JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11331870", "url": "https://glygen.org/publication/PubMed/11331870", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9360983", "url": "https://glygen.org/publication/PubMed/9360983", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11314030", "url": "https://glygen.org/publication/PubMed/11314030", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12370821", "url": "https://glygen.org/publication/PubMed/12370821", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7509446", "url": "https://glygen.org/publication/PubMed/7509446", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27790061", "url": "https://glygen.org/publication/PubMed/27790061", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10816598", "url": "https://glygen.org/publication/PubMed/10816598", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17828307", "url": "https://glygen.org/publication/PubMed/17828307", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q05397*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "27178753", "url": "https://glygen.org/publication/PubMed/27178753", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "10047444", "url": "https://glygen.org/publication/PubMed/10047444", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10212207", "url": "https://glygen.org/publication/PubMed/10212207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10400703", "url": "https://glygen.org/publication/PubMed/10400703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10769034", "url": "https://glygen.org/publication/PubMed/10769034", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10856226", "url": "https://glygen.org/publication/PubMed/10856226", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10958798", "url": "https://glygen.org/publication/PubMed/10958798", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10998418", "url": "https://glygen.org/publication/PubMed/10998418", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11119718", "url": "https://glygen.org/publication/PubMed/11119718", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11278488", "url": "https://glygen.org/publication/PubMed/11278488", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11313859", "url": "https://glygen.org/publication/PubMed/11313859", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11438458", "url": "https://glygen.org/publication/PubMed/11438458", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11448998", "url": "https://glygen.org/publication/PubMed/11448998", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11572981", "url": "https://glygen.org/publication/PubMed/11572981", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11585739", "url": "https://glygen.org/publication/PubMed/11585739", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11602246", "url": "https://glygen.org/publication/PubMed/11602246", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11606050", "url": "https://glygen.org/publication/PubMed/11606050", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11668182", "url": "https://glygen.org/publication/PubMed/11668182", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11696015", "url": "https://glygen.org/publication/PubMed/11696015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11787067", "url": "https://glygen.org/publication/PubMed/11787067", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11807823", "url": "https://glygen.org/publication/PubMed/11807823", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11891289", "url": "https://glygen.org/publication/PubMed/11891289", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11909938", "url": "https://glygen.org/publication/PubMed/11909938", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12021278", "url": "https://glygen.org/publication/PubMed/12021278", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12084011", "url": "https://glygen.org/publication/PubMed/12084011", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12215217", "url": "https://glygen.org/publication/PubMed/12215217", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12370243", "url": "https://glygen.org/publication/PubMed/12370243", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12391143", "url": "https://glygen.org/publication/PubMed/12391143", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12558988", "url": "https://glygen.org/publication/PubMed/12558988", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12615911", "url": "https://glygen.org/publication/PubMed/12615911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12640026", "url": "https://glygen.org/publication/PubMed/12640026", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12700132", "url": "https://glygen.org/publication/PubMed/12700132", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12730223", "url": "https://glygen.org/publication/PubMed/12730223", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12738990", "url": "https://glygen.org/publication/PubMed/12738990", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12761229", "url": "https://glygen.org/publication/PubMed/12761229", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12838315", "url": "https://glygen.org/publication/PubMed/12838315", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12871985", "url": "https://glygen.org/publication/PubMed/12871985", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12876277", "url": "https://glygen.org/publication/PubMed/12876277", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12876384", "url": "https://glygen.org/publication/PubMed/12876384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12960434", "url": "https://glygen.org/publication/PubMed/12960434", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14500712", "url": "https://glygen.org/publication/PubMed/14500712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14603053", "url": "https://glygen.org/publication/PubMed/14603053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14604860", "url": "https://glygen.org/publication/PubMed/14604860", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14610060", "url": "https://glygen.org/publication/PubMed/14610060", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14666664", "url": "https://glygen.org/publication/PubMed/14666664", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14670178", "url": "https://glygen.org/publication/PubMed/14670178", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14703945", "url": "https://glygen.org/publication/PubMed/14703945", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14712221", "url": "https://glygen.org/publication/PubMed/14712221", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14761895", "url": "https://glygen.org/publication/PubMed/14761895", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14978737", "url": "https://glygen.org/publication/PubMed/14978737", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15126359", "url": "https://glygen.org/publication/PubMed/15126359", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15138291", "url": "https://glygen.org/publication/PubMed/15138291", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15210734", "url": "https://glygen.org/publication/PubMed/15210734", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15242759", "url": "https://glygen.org/publication/PubMed/15242759", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15246682", "url": "https://glygen.org/publication/PubMed/15246682", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15331608", "url": "https://glygen.org/publication/PubMed/15331608", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15598735", "url": "https://glygen.org/publication/PubMed/15598735", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15611137", "url": "https://glygen.org/publication/PubMed/15611137", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15625302", "url": "https://glygen.org/publication/PubMed/15625302", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15707572", "url": "https://glygen.org/publication/PubMed/15707572", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15707596", "url": "https://glygen.org/publication/PubMed/15707596", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15785954", "url": "https://glygen.org/publication/PubMed/15785954", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15817454", "url": "https://glygen.org/publication/PubMed/15817454", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15890789", "url": "https://glygen.org/publication/PubMed/15890789", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15963258", "url": "https://glygen.org/publication/PubMed/15963258", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16039608", "url": "https://glygen.org/publication/PubMed/16039608", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16159962", "url": "https://glygen.org/publication/PubMed/16159962", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16195476", "url": "https://glygen.org/publication/PubMed/16195476", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16253116", "url": "https://glygen.org/publication/PubMed/16253116", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16267008", "url": "https://glygen.org/publication/PubMed/16267008", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16415178", "url": "https://glygen.org/publication/PubMed/16415178", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16461767", "url": "https://glygen.org/publication/PubMed/16461767", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16473349", "url": "https://glygen.org/publication/PubMed/16473349", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16523241", "url": "https://glygen.org/publication/PubMed/16523241", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16574795", "url": "https://glygen.org/publication/PubMed/16574795", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16728403", "url": "https://glygen.org/publication/PubMed/16728403", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16847103", "url": "https://glygen.org/publication/PubMed/16847103", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16912186", "url": "https://glygen.org/publication/PubMed/16912186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16920701", "url": "https://glygen.org/publication/PubMed/16920701", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16998832", "url": "https://glygen.org/publication/PubMed/16998832", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17081517", "url": "https://glygen.org/publication/PubMed/17081517", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17088251", "url": "https://glygen.org/publication/PubMed/17088251", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17096371", "url": "https://glygen.org/publication/PubMed/17096371", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17215324", "url": "https://glygen.org/publication/PubMed/17215324", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17234774", "url": "https://glygen.org/publication/PubMed/17234774", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17234784", "url": "https://glygen.org/publication/PubMed/17234784", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17395594", "url": "https://glygen.org/publication/PubMed/17395594", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17431114", "url": "https://glygen.org/publication/PubMed/17431114", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17497960", "url": "https://glygen.org/publication/PubMed/17497960", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17524523", "url": "https://glygen.org/publication/PubMed/17524523", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17721515", "url": "https://glygen.org/publication/PubMed/17721515", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17898132", "url": "https://glygen.org/publication/PubMed/17898132", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18006843", "url": "https://glygen.org/publication/PubMed/18006843", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18032789", "url": "https://glygen.org/publication/PubMed/18032789", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18198129", "url": "https://glygen.org/publication/PubMed/18198129", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18314876", "url": "https://glygen.org/publication/PubMed/18314876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18382658", "url": "https://glygen.org/publication/PubMed/18382658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18562041", "url": "https://glygen.org/publication/PubMed/18562041", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18676832", "url": "https://glygen.org/publication/PubMed/18676832", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18757826", "url": "https://glygen.org/publication/PubMed/18757826", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18774960", "url": "https://glygen.org/publication/PubMed/18774960", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18922173", "url": "https://glygen.org/publication/PubMed/18922173", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18923058", "url": "https://glygen.org/publication/PubMed/18923058", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18930841", "url": "https://glygen.org/publication/PubMed/18930841", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18989950", "url": "https://glygen.org/publication/PubMed/18989950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19029090", "url": "https://glygen.org/publication/PubMed/19029090", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19260479", "url": "https://glygen.org/publication/PubMed/19260479", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19294408", "url": "https://glygen.org/publication/PubMed/19294408", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19297531", "url": "https://glygen.org/publication/PubMed/19297531", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19553453", "url": "https://glygen.org/publication/PubMed/19553453", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19671193", "url": "https://glygen.org/publication/PubMed/19671193", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19695571", "url": "https://glygen.org/publication/PubMed/19695571", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19787193", "url": "https://glygen.org/publication/PubMed/19787193", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19826415", "url": "https://glygen.org/publication/PubMed/19826415", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19834610", "url": "https://glygen.org/publication/PubMed/19834610", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19931412", "url": "https://glygen.org/publication/PubMed/19931412", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20021699", "url": "https://glygen.org/publication/PubMed/20021699", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20082722", "url": "https://glygen.org/publication/PubMed/20082722", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20122724", "url": "https://glygen.org/publication/PubMed/20122724", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20160475", "url": "https://glygen.org/publication/PubMed/20160475", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20180147", "url": "https://glygen.org/publication/PubMed/20180147", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20224789", "url": "https://glygen.org/publication/PubMed/20224789", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20308429", "url": "https://glygen.org/publication/PubMed/20308429", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20354780", "url": "https://glygen.org/publication/PubMed/20354780", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20357007", "url": "https://glygen.org/publication/PubMed/20357007", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20527022", "url": "https://glygen.org/publication/PubMed/20527022", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20621036", "url": "https://glygen.org/publication/PubMed/20621036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20657775", "url": "https://glygen.org/publication/PubMed/20657775", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20713357", "url": "https://glygen.org/publication/PubMed/20713357", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20724588", "url": "https://glygen.org/publication/PubMed/20724588", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20802517", "url": "https://glygen.org/publication/PubMed/20802517", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20847951", "url": "https://glygen.org/publication/PubMed/20847951", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21073482", "url": "https://glygen.org/publication/PubMed/21073482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21119598", "url": "https://glygen.org/publication/PubMed/21119598", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21209368", "url": "https://glygen.org/publication/PubMed/21209368", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21344482", "url": "https://glygen.org/publication/PubMed/21344482", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21359179", "url": "https://glygen.org/publication/PubMed/21359179", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21401419", "url": "https://glygen.org/publication/PubMed/21401419", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21408150", "url": "https://glygen.org/publication/PubMed/21408150", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21426305", "url": "https://glygen.org/publication/PubMed/21426305", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21556755", "url": "https://glygen.org/publication/PubMed/21556755", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21660950", "url": "https://glygen.org/publication/PubMed/21660950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21887232", "url": "https://glygen.org/publication/PubMed/21887232", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21898412", "url": "https://glygen.org/publication/PubMed/21898412", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21903606", "url": "https://glygen.org/publication/PubMed/21903606", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21967109", "url": "https://glygen.org/publication/PubMed/21967109", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22042621", "url": "https://glygen.org/publication/PubMed/22042621", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22069492", "url": "https://glygen.org/publication/PubMed/22069492", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22070920", "url": "https://glygen.org/publication/PubMed/22070920", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22078467", "url": "https://glygen.org/publication/PubMed/22078467", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22136719", "url": "https://glygen.org/publication/PubMed/22136719", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22149259", "url": "https://glygen.org/publication/PubMed/22149259", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22174684", "url": "https://glygen.org/publication/PubMed/22174684", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22194972", "url": "https://glygen.org/publication/PubMed/22194972", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22216254", "url": "https://glygen.org/publication/PubMed/22216254", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22267972", "url": "https://glygen.org/publication/PubMed/22267972", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22270917", "url": "https://glygen.org/publication/PubMed/22270917", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22319618", "url": "https://glygen.org/publication/PubMed/22319618", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22550026", "url": "https://glygen.org/publication/PubMed/22550026", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22641287", "url": "https://glygen.org/publication/PubMed/22641287", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22710722", "url": "https://glygen.org/publication/PubMed/22710722", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22734001", "url": "https://glygen.org/publication/PubMed/22734001", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22766511", "url": "https://glygen.org/publication/PubMed/22766511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22810307", "url": "https://glygen.org/publication/PubMed/22810307", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22876288", "url": "https://glygen.org/publication/PubMed/22876288", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22952866", "url": "https://glygen.org/publication/PubMed/22952866", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22982417", "url": "https://glygen.org/publication/PubMed/22982417", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23102268", "url": "https://glygen.org/publication/PubMed/23102268", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23109808", "url": "https://glygen.org/publication/PubMed/23109808", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23128389", "url": "https://glygen.org/publication/PubMed/23128389", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23272972", "url": "https://glygen.org/publication/PubMed/23272972", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23339185", "url": "https://glygen.org/publication/PubMed/23339185", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23357870", "url": "https://glygen.org/publication/PubMed/23357870", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23485561", "url": "https://glygen.org/publication/PubMed/23485561", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23515360", "url": "https://glygen.org/publication/PubMed/23515360", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23525457", "url": "https://glygen.org/publication/PubMed/23525457", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23681745", "url": "https://glygen.org/publication/PubMed/23681745", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23755096", "url": "https://glygen.org/publication/PubMed/23755096", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23755149", "url": "https://glygen.org/publication/PubMed/23755149", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23792569", "url": "https://glygen.org/publication/PubMed/23792569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23812425", "url": "https://glygen.org/publication/PubMed/23812425", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23836527", "url": "https://glygen.org/publication/PubMed/23836527", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23858760", "url": "https://glygen.org/publication/PubMed/23858760", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23874694", "url": "https://glygen.org/publication/PubMed/23874694", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23984323", "url": "https://glygen.org/publication/PubMed/23984323", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24010829", "url": "https://glygen.org/publication/PubMed/24010829", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24025096", "url": "https://glygen.org/publication/PubMed/24025096", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24039840", "url": "https://glygen.org/publication/PubMed/24039840", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24039841", "url": "https://glygen.org/publication/PubMed/24039841", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24040310", "url": "https://glygen.org/publication/PubMed/24040310", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24058594", "url": "https://glygen.org/publication/PubMed/24058594", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24062525", "url": "https://glygen.org/publication/PubMed/24062525", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24083092", "url": "https://glygen.org/publication/PubMed/24083092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24121667", "url": "https://glygen.org/publication/PubMed/24121667", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24123071", "url": "https://glygen.org/publication/PubMed/24123071", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24194567", "url": "https://glygen.org/publication/PubMed/24194567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24201748", "url": "https://glygen.org/publication/PubMed/24201748", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24260201", "url": "https://glygen.org/publication/PubMed/24260201", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24290759", "url": "https://glygen.org/publication/PubMed/24290759", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24294595", "url": "https://glygen.org/publication/PubMed/24294595", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24360952", "url": "https://glygen.org/publication/PubMed/24360952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24370784", "url": "https://glygen.org/publication/PubMed/24370784", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24381802", "url": "https://glygen.org/publication/PubMed/24381802", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24409152", "url": "https://glygen.org/publication/PubMed/24409152", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24533083", "url": "https://glygen.org/publication/PubMed/24533083", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24586773", "url": "https://glygen.org/publication/PubMed/24586773", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24632806", "url": "https://glygen.org/publication/PubMed/24632806", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24655477", "url": "https://glygen.org/publication/PubMed/24655477", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24706070", "url": "https://glygen.org/publication/PubMed/24706070", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24772088", "url": "https://glygen.org/publication/PubMed/24772088", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24786638", "url": "https://glygen.org/publication/PubMed/24786638", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24858039", "url": "https://glygen.org/publication/PubMed/24858039", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24863845", "url": "https://glygen.org/publication/PubMed/24863845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24894151", "url": "https://glygen.org/publication/PubMed/24894151", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24911159", "url": "https://glygen.org/publication/PubMed/24911159", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24999733", "url": "https://glygen.org/publication/PubMed/24999733", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25056351", "url": "https://glygen.org/publication/PubMed/25056351", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25113248", "url": "https://glygen.org/publication/PubMed/25113248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25187949", "url": "https://glygen.org/publication/PubMed/25187949", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25226367", "url": "https://glygen.org/publication/PubMed/25226367", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25277206", "url": "https://glygen.org/publication/PubMed/25277206", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25300309", "url": "https://glygen.org/publication/PubMed/25300309", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25313365", "url": "https://glygen.org/publication/PubMed/25313365", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25351103", "url": "https://glygen.org/publication/PubMed/25351103", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25428919", "url": "https://glygen.org/publication/PubMed/25428919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25486573", "url": "https://glygen.org/publication/PubMed/25486573", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25539072", "url": "https://glygen.org/publication/PubMed/25539072", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25617898", "url": "https://glygen.org/publication/PubMed/25617898", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25631868", "url": "https://glygen.org/publication/PubMed/25631868", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25705585", "url": "https://glygen.org/publication/PubMed/25705585", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25708150", "url": "https://glygen.org/publication/PubMed/25708150", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25749031", "url": "https://glygen.org/publication/PubMed/25749031", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25868388", "url": "https://glygen.org/publication/PubMed/25868388", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25880415", "url": "https://glygen.org/publication/PubMed/25880415", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25889845", "url": "https://glygen.org/publication/PubMed/25889845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25890707", "url": "https://glygen.org/publication/PubMed/25890707", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25947155", "url": "https://glygen.org/publication/PubMed/25947155", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25958313", "url": "https://glygen.org/publication/PubMed/25958313", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25978354", "url": "https://glygen.org/publication/PubMed/25978354", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25980494", "url": "https://glygen.org/publication/PubMed/25980494", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26004127", "url": "https://glygen.org/publication/PubMed/26004127", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26079101", "url": "https://glygen.org/publication/PubMed/26079101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26110647", "url": "https://glygen.org/publication/PubMed/26110647", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26119934", "url": "https://glygen.org/publication/PubMed/26119934", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26172215", "url": "https://glygen.org/publication/PubMed/26172215", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26216901", "url": "https://glygen.org/publication/PubMed/26216901", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26230358", "url": "https://glygen.org/publication/PubMed/26230358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26245992", "url": "https://glygen.org/publication/PubMed/26245992", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26294392", "url": "https://glygen.org/publication/PubMed/26294392", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26300973", "url": "https://glygen.org/publication/PubMed/26300973", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26365310", "url": "https://glygen.org/publication/PubMed/26365310", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26375443", "url": "https://glygen.org/publication/PubMed/26375443", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26377974", "url": "https://glygen.org/publication/PubMed/26377974", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26393679", "url": "https://glygen.org/publication/PubMed/26393679", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26406376", "url": "https://glygen.org/publication/PubMed/26406376", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26456697", "url": "https://glygen.org/publication/PubMed/26456697", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26501082", "url": "https://glygen.org/publication/PubMed/26501082", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26542021", "url": "https://glygen.org/publication/PubMed/26542021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26546726", "url": "https://glygen.org/publication/PubMed/26546726", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26549523", "url": "https://glygen.org/publication/PubMed/26549523", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26556867", "url": "https://glygen.org/publication/PubMed/26556867", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26649283", "url": "https://glygen.org/publication/PubMed/26649283", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26689988", "url": "https://glygen.org/publication/PubMed/26689988", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26700725", "url": "https://glygen.org/publication/PubMed/26700725", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26703626", "url": "https://glygen.org/publication/PubMed/26703626", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26751774", "url": "https://glygen.org/publication/PubMed/26751774", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26752742", "url": "https://glygen.org/publication/PubMed/26752742", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26788094", "url": "https://glygen.org/publication/PubMed/26788094", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26821125", "url": "https://glygen.org/publication/PubMed/26821125", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26833789", "url": "https://glygen.org/publication/PubMed/26833789", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26842895", "url": "https://glygen.org/publication/PubMed/26842895", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26848618", "url": "https://glygen.org/publication/PubMed/26848618", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26893679", "url": "https://glygen.org/publication/PubMed/26893679", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26931461", "url": "https://glygen.org/publication/PubMed/26931461", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26961176", "url": "https://glygen.org/publication/PubMed/26961176", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26975850", "url": "https://glygen.org/publication/PubMed/26975850", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26984508", "url": "https://glygen.org/publication/PubMed/26984508", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26984511", "url": "https://glygen.org/publication/PubMed/26984511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26988603", "url": "https://glygen.org/publication/PubMed/26988603", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26993780", "url": "https://glygen.org/publication/PubMed/26993780", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27191259", "url": "https://glygen.org/publication/PubMed/27191259", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27220365", "url": "https://glygen.org/publication/PubMed/27220365", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27237320", "url": "https://glygen.org/publication/PubMed/27237320", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27246739", "url": "https://glygen.org/publication/PubMed/27246739", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27248472", "url": "https://glygen.org/publication/PubMed/27248472", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27278471", "url": "https://glygen.org/publication/PubMed/27278471", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27344177", "url": "https://glygen.org/publication/PubMed/27344177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27363027", "url": "https://glygen.org/publication/PubMed/27363027", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27402964", "url": "https://glygen.org/publication/PubMed/27402964", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27428469", "url": "https://glygen.org/publication/PubMed/27428469", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27460083", "url": "https://glygen.org/publication/PubMed/27460083", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27462783", "url": "https://glygen.org/publication/PubMed/27462783", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27467982", "url": "https://glygen.org/publication/PubMed/27467982", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27487141", "url": "https://glygen.org/publication/PubMed/27487141", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27542844", "url": "https://glygen.org/publication/PubMed/27542844", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27567948", "url": "https://glygen.org/publication/PubMed/27567948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27602495", "url": "https://glygen.org/publication/PubMed/27602495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27611942", "url": "https://glygen.org/publication/PubMed/27611942", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27638858", "url": "https://glygen.org/publication/PubMed/27638858", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27715394", "url": "https://glygen.org/publication/PubMed/27715394", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27845385", "url": "https://glygen.org/publication/PubMed/27845385", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28053698", "url": "https://glygen.org/publication/PubMed/28053698", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28068967", "url": "https://glygen.org/publication/PubMed/28068967", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28076322", "url": "https://glygen.org/publication/PubMed/28076322", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28124908", "url": "https://glygen.org/publication/PubMed/28124908", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28134933", "url": "https://glygen.org/publication/PubMed/28134933", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28188308", "url": "https://glygen.org/publication/PubMed/28188308", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28225063", "url": "https://glygen.org/publication/PubMed/28225063", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28257035", "url": "https://glygen.org/publication/PubMed/28257035", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28338656", "url": "https://glygen.org/publication/PubMed/28338656", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28361970", "url": "https://glygen.org/publication/PubMed/28361970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28398603", "url": "https://glygen.org/publication/PubMed/28398603", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28406574", "url": "https://glygen.org/publication/PubMed/28406574", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28415713", "url": "https://glygen.org/publication/PubMed/28415713", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28423580", "url": "https://glygen.org/publication/PubMed/28423580", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28445805", "url": "https://glygen.org/publication/PubMed/28445805", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28450296", "url": "https://glygen.org/publication/PubMed/28450296", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28459432", "url": "https://glygen.org/publication/PubMed/28459432", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28507287", "url": "https://glygen.org/publication/PubMed/28507287", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28542214", "url": "https://glygen.org/publication/PubMed/28542214", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28624785", "url": "https://glygen.org/publication/PubMed/28624785", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28642549", "url": "https://glygen.org/publication/PubMed/28642549", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28667800", "url": "https://glygen.org/publication/PubMed/28667800", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28715434", "url": "https://glygen.org/publication/PubMed/28715434", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28741790", "url": "https://glygen.org/publication/PubMed/28741790", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29021002", "url": "https://glygen.org/publication/PubMed/29021002", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29036202", "url": "https://glygen.org/publication/PubMed/29036202", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29039492", "url": "https://glygen.org/publication/PubMed/29039492", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29046395", "url": "https://glygen.org/publication/PubMed/29046395", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29066806", "url": "https://glygen.org/publication/PubMed/29066806", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29088849", "url": "https://glygen.org/publication/PubMed/29088849", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29151962", "url": "https://glygen.org/publication/PubMed/29151962", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29158989", "url": "https://glygen.org/publication/PubMed/29158989", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29186907", "url": "https://glygen.org/publication/PubMed/29186907", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29190494", "url": "https://glygen.org/publication/PubMed/29190494", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29228673", "url": "https://glygen.org/publication/PubMed/29228673", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29263678", "url": "https://glygen.org/publication/PubMed/29263678", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29276408", "url": "https://glygen.org/publication/PubMed/29276408", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29311227", "url": "https://glygen.org/publication/PubMed/29311227", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29382358", "url": "https://glygen.org/publication/PubMed/29382358", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29422613", "url": "https://glygen.org/publication/PubMed/29422613", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29434841", "url": "https://glygen.org/publication/PubMed/29434841", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29484384", "url": "https://glygen.org/publication/PubMed/29484384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29491429", "url": "https://glygen.org/publication/PubMed/29491429", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29535802", "url": "https://glygen.org/publication/PubMed/29535802", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29563383", "url": "https://glygen.org/publication/PubMed/29563383", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29593542", "url": "https://glygen.org/publication/PubMed/29593542", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29700289", "url": "https://glygen.org/publication/PubMed/29700289", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29728077", "url": "https://glygen.org/publication/PubMed/29728077", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29740072", "url": "https://glygen.org/publication/PubMed/29740072", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29752441", "url": "https://glygen.org/publication/PubMed/29752441", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29791208", "url": "https://glygen.org/publication/PubMed/29791208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29796177", "url": "https://glygen.org/publication/PubMed/29796177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29903032", "url": "https://glygen.org/publication/PubMed/29903032", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29986550", "url": "https://glygen.org/publication/PubMed/29986550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29993014", "url": "https://glygen.org/publication/PubMed/29993014", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30013514", "url": "https://glygen.org/publication/PubMed/30013514", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30033448", "url": "https://glygen.org/publication/PubMed/30033448", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30055645", "url": "https://glygen.org/publication/PubMed/30055645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30065198", "url": "https://glygen.org/publication/PubMed/30065198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30087707", "url": "https://glygen.org/publication/PubMed/30087707", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30166526", "url": "https://glygen.org/publication/PubMed/30166526", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30332774", "url": "https://glygen.org/publication/PubMed/30332774", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30337877", "url": "https://glygen.org/publication/PubMed/30337877", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30387148", "url": "https://glygen.org/publication/PubMed/30387148", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30458784", "url": "https://glygen.org/publication/PubMed/30458784", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30464516", "url": "https://glygen.org/publication/PubMed/30464516", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30488595", "url": "https://glygen.org/publication/PubMed/30488595", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30531837", "url": "https://glygen.org/publication/PubMed/30531837", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30539198", "url": "https://glygen.org/publication/PubMed/30539198", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30555628", "url": "https://glygen.org/publication/PubMed/30555628", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30563275", "url": "https://glygen.org/publication/PubMed/30563275", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30571746", "url": "https://glygen.org/publication/PubMed/30571746", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30696915", "url": "https://glygen.org/publication/PubMed/30696915", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30717801", "url": "https://glygen.org/publication/PubMed/30717801", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30728047", "url": "https://glygen.org/publication/PubMed/30728047", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30742951", "url": "https://glygen.org/publication/PubMed/30742951", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30744493", "url": "https://glygen.org/publication/PubMed/30744493", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30779783", "url": "https://glygen.org/publication/PubMed/30779783", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30816469", "url": "https://glygen.org/publication/PubMed/30816469", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30836148", "url": "https://glygen.org/publication/PubMed/30836148", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30894654", "url": "https://glygen.org/publication/PubMed/30894654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30920523", "url": "https://glygen.org/publication/PubMed/30920523", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31060904", "url": "https://glygen.org/publication/PubMed/31060904", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31160603", "url": "https://glygen.org/publication/PubMed/31160603", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31170089", "url": "https://glygen.org/publication/PubMed/31170089", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31186741", "url": "https://glygen.org/publication/PubMed/31186741", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31297342", "url": "https://glygen.org/publication/PubMed/31297342", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31383893", "url": "https://glygen.org/publication/PubMed/31383893", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31420553", "url": "https://glygen.org/publication/PubMed/31420553", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31428520", "url": "https://glygen.org/publication/PubMed/31428520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31478830", "url": "https://glygen.org/publication/PubMed/31478830", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31480645", "url": "https://glygen.org/publication/PubMed/31480645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31501460", "url": "https://glygen.org/publication/PubMed/31501460", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31516757", "url": "https://glygen.org/publication/PubMed/31516757", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31519958", "url": "https://glygen.org/publication/PubMed/31519958", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31554180", "url": "https://glygen.org/publication/PubMed/31554180", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31565187", "url": "https://glygen.org/publication/PubMed/31565187", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31627430", "url": "https://glygen.org/publication/PubMed/31627430", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31648990", "url": "https://glygen.org/publication/PubMed/31648990", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31652779", "url": "https://glygen.org/publication/PubMed/31652779", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31654241", "url": "https://glygen.org/publication/PubMed/31654241", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31671889", "url": "https://glygen.org/publication/PubMed/31671889", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31831830", "url": "https://glygen.org/publication/PubMed/31831830", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31867162", "url": "https://glygen.org/publication/PubMed/31867162", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31870092", "url": "https://glygen.org/publication/PubMed/31870092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31926619", "url": "https://glygen.org/publication/PubMed/31926619", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32155953", "url": "https://glygen.org/publication/PubMed/32155953", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32256987", "url": "https://glygen.org/publication/PubMed/32256987", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32286266", "url": "https://glygen.org/publication/PubMed/32286266", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32337793", "url": "https://glygen.org/publication/PubMed/32337793", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32415208", "url": "https://glygen.org/publication/PubMed/32415208", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32604782", "url": "https://glygen.org/publication/PubMed/32604782", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32733919", "url": "https://glygen.org/publication/PubMed/32733919", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32784087", "url": "https://glygen.org/publication/PubMed/32784087", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32806748", "url": "https://glygen.org/publication/PubMed/32806748", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32844749", "url": "https://glygen.org/publication/PubMed/32844749", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32848136", "url": "https://glygen.org/publication/PubMed/32848136", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32850845", "url": "https://glygen.org/publication/PubMed/32850845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32872257", "url": "https://glygen.org/publication/PubMed/32872257", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33025708", "url": "https://glygen.org/publication/PubMed/33025708", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33036231", "url": "https://glygen.org/publication/PubMed/33036231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33076263", "url": "https://glygen.org/publication/PubMed/33076263", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33287873", "url": "https://glygen.org/publication/PubMed/33287873", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33420364", "url": "https://glygen.org/publication/PubMed/33420364", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33532186", "url": "https://glygen.org/publication/PubMed/33532186", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33634070", "url": "https://glygen.org/publication/PubMed/33634070", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33668531", "url": "https://glygen.org/publication/PubMed/33668531", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33715263", "url": "https://glygen.org/publication/PubMed/33715263", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33724150", "url": "https://glygen.org/publication/PubMed/33724150", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33750427", "url": "https://glygen.org/publication/PubMed/33750427", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33799345", "url": "https://glygen.org/publication/PubMed/33799345", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33846818", "url": "https://glygen.org/publication/PubMed/33846818", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33898431", "url": "https://glygen.org/publication/PubMed/33898431", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33981002", "url": "https://glygen.org/publication/PubMed/33981002", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35201437", "url": "https://glygen.org/publication/PubMed/35201437", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35257717", "url": "https://glygen.org/publication/PubMed/35257717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35426066", "url": "https://glygen.org/publication/PubMed/35426066", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35962191", "url": "https://glygen.org/publication/PubMed/35962191", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35982848", "url": "https://glygen.org/publication/PubMed/35982848", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36009384", "url": "https://glygen.org/publication/PubMed/36009384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7553664", "url": "https://glygen.org/publication/PubMed/7553664", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7739563", "url": "https://glygen.org/publication/PubMed/7739563", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8051157", "url": "https://glygen.org/publication/PubMed/8051157", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8824286", "url": "https://glygen.org/publication/PubMed/8824286", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9148935", "url": "https://glygen.org/publication/PubMed/9148935", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9416004", "url": "https://glygen.org/publication/PubMed/9416004", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9922457", "url": "https://glygen.org/publication/PubMed/9922457", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ANSEKQGMRTHAVSVSETDD", "down_seq": "AEIIDEEDTYTMPSTRDYEI", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Abolishes autophosphorylation. Abolishes interaction with SRC and activation of BMX. Reduces phosphorylation of NEDD9.", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "11331870", "url": "https://glygen.org/publication/PubMed/11331870" }, { "database": "PubMed", "id": "9360983", "url": "https://glygen.org/publication/PubMed/9360983" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "P09769-1", "kinase_gene_name": "FGR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "P46108-1", "kinase_gene_name": "CRK", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11314030", "url": "https://glygen.org/publication/PubMed/11314030" }, { "database": "PubMed", "id": "12370821", "url": "https://glygen.org/publication/PubMed/12370821" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7509446", "url": "https://glygen.org/publication/PubMed/7509446" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11314030", "url": "https://glygen.org/publication/PubMed/11314030" }, { "database": "PubMed", "id": "12370821", "url": "https://glygen.org/publication/PubMed/12370821" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7509446", "url": "https://glygen.org/publication/PubMed/7509446" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "27790061", "url": "https://glygen.org/publication/PubMed/27790061" }, { "database": "PubMed", "id": "10816598", "url": "https://glygen.org/publication/PubMed/10816598" }, { "database": "PubMed", "id": "17828307", "url": "https://glygen.org/publication/PubMed/17828307" }, { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ], "site_lbl": "Tyr397" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by autocatalysis", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11314030", "url": "https://glygen.org/publication/PubMed/11314030" }, { "database": "PubMed", "id": "12370821", "url": "https://glygen.org/publication/PubMed/12370821" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7509446", "url": "https://glygen.org/publication/PubMed/7509446" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "IntAct", "id": "Q05397", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q05397*" }, { "database": "PubMed", "id": "27178753", "url": "https://glygen.org/publication/PubMed/27178753" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "PubMed", "id": "10047444", "url": "https://glygen.org/publication/PubMed/10047444" }, { "database": "PubMed", "id": "10212207", "url": "https://glygen.org/publication/PubMed/10212207" }, { "database": "PubMed", "id": "10400703", "url": "https://glygen.org/publication/PubMed/10400703" }, { "database": "PubMed", "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902" }, { "database": "PubMed", "id": "10769034", "url": "https://glygen.org/publication/PubMed/10769034" }, { "database": "PubMed", "id": "10816598", "url": "https://glygen.org/publication/PubMed/10816598" }, { "database": "PubMed", "id": "10856226", "url": "https://glygen.org/publication/PubMed/10856226" }, { "database": "PubMed", "id": "10958798", "url": "https://glygen.org/publication/PubMed/10958798" }, { "database": "PubMed", "id": "10998418", "url": "https://glygen.org/publication/PubMed/10998418" }, { "database": "PubMed", "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591" }, { "database": "PubMed", "id": "11119718", "url": "https://glygen.org/publication/PubMed/11119718" }, { "database": "PubMed", "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924" }, { "database": "PubMed", "id": "11278488", "url": "https://glygen.org/publication/PubMed/11278488" }, { "database": "PubMed", "id": "11313859", "url": "https://glygen.org/publication/PubMed/11313859" }, { "database": "PubMed", "id": "11438458", "url": "https://glygen.org/publication/PubMed/11438458" }, { "database": "PubMed", "id": "11448998", "url": "https://glygen.org/publication/PubMed/11448998" }, { "database": "PubMed", "id": "11572981", "url": "https://glygen.org/publication/PubMed/11572981" }, { "database": "PubMed", "id": "11585739", "url": "https://glygen.org/publication/PubMed/11585739" }, { "database": "PubMed", "id": "11602246", "url": "https://glygen.org/publication/PubMed/11602246" }, { "database": "PubMed", "id": "11606050", "url": "https://glygen.org/publication/PubMed/11606050" }, { "database": "PubMed", "id": "11668182", "url": "https://glygen.org/publication/PubMed/11668182" }, { "database": "PubMed", "id": "11696015", "url": "https://glygen.org/publication/PubMed/11696015" }, { "database": "PubMed", "id": "11787067", "url": "https://glygen.org/publication/PubMed/11787067" }, { "database": "PubMed", "id": "11807823", "url": "https://glygen.org/publication/PubMed/11807823" }, { "database": "PubMed", "id": "11891289", "url": "https://glygen.org/publication/PubMed/11891289" }, { "database": "PubMed", "id": "11909938", "url": "https://glygen.org/publication/PubMed/11909938" }, { "database": "PubMed", "id": "12021278", "url": "https://glygen.org/publication/PubMed/12021278" }, { "database": "PubMed", "id": "12084011", "url": "https://glygen.org/publication/PubMed/12084011" }, { "database": "PubMed", "id": "12215217", "url": "https://glygen.org/publication/PubMed/12215217" }, { "database": "PubMed", "id": "12370243", "url": "https://glygen.org/publication/PubMed/12370243" }, { "database": "PubMed", "id": "12391143", "url": "https://glygen.org/publication/PubMed/12391143" }, { "database": "PubMed", "id": "12558988", "url": "https://glygen.org/publication/PubMed/12558988" }, { "database": "PubMed", "id": "12615911", "url": "https://glygen.org/publication/PubMed/12615911" }, { "database": "PubMed", "id": "12640026", "url": "https://glygen.org/publication/PubMed/12640026" }, { "database": "PubMed", "id": "12700132", "url": "https://glygen.org/publication/PubMed/12700132" }, { "database": "PubMed", "id": "12730223", "url": "https://glygen.org/publication/PubMed/12730223" }, { "database": "PubMed", "id": "12738990", "url": "https://glygen.org/publication/PubMed/12738990" }, { "database": "PubMed", "id": "12761229", "url": "https://glygen.org/publication/PubMed/12761229" }, { "database": "PubMed", "id": "12838315", "url": "https://glygen.org/publication/PubMed/12838315" }, { "database": "PubMed", "id": "12871985", "url": "https://glygen.org/publication/PubMed/12871985" }, { "database": "PubMed", "id": "12876277", "url": "https://glygen.org/publication/PubMed/12876277" }, { "database": "PubMed", "id": "12876384", "url": "https://glygen.org/publication/PubMed/12876384" }, { "database": "PubMed", "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054" }, { "database": "PubMed", "id": "12960434", "url": "https://glygen.org/publication/PubMed/12960434" }, { "database": "PubMed", "id": "14500712", "url": "https://glygen.org/publication/PubMed/14500712" }, { "database": "PubMed", "id": "14603053", "url": "https://glygen.org/publication/PubMed/14603053" }, { "database": "PubMed", "id": "14604860", "url": "https://glygen.org/publication/PubMed/14604860" }, { "database": "PubMed", "id": "14610060", "url": "https://glygen.org/publication/PubMed/14610060" }, { "database": "PubMed", "id": "14666664", "url": "https://glygen.org/publication/PubMed/14666664" }, { "database": "PubMed", "id": "14670178", "url": "https://glygen.org/publication/PubMed/14670178" }, { "database": "PubMed", "id": "14703945", "url": "https://glygen.org/publication/PubMed/14703945" }, { "database": "PubMed", "id": "14712221", "url": "https://glygen.org/publication/PubMed/14712221" }, { "database": "PubMed", "id": "14761895", "url": "https://glygen.org/publication/PubMed/14761895" }, { "database": "PubMed", "id": "14978737", "url": "https://glygen.org/publication/PubMed/14978737" }, { "database": "PubMed", "id": "15126359", "url": "https://glygen.org/publication/PubMed/15126359" }, { "database": "PubMed", "id": "15138291", "url": "https://glygen.org/publication/PubMed/15138291" }, { "database": "PubMed", "id": "15210734", "url": "https://glygen.org/publication/PubMed/15210734" }, { "database": "PubMed", "id": "15242759", "url": "https://glygen.org/publication/PubMed/15242759" }, { "database": "PubMed", "id": "15246682", "url": "https://glygen.org/publication/PubMed/15246682" }, { "database": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" }, { "database": "PubMed", "id": "15331608", "url": "https://glygen.org/publication/PubMed/15331608" }, { "database": "PubMed", "id": "15598735", "url": "https://glygen.org/publication/PubMed/15598735" }, { "database": "PubMed", "id": "15611137", "url": "https://glygen.org/publication/PubMed/15611137" }, { "database": "PubMed", "id": "15625302", "url": "https://glygen.org/publication/PubMed/15625302" }, { "database": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" }, { "database": "PubMed", "id": "15707572", "url": "https://glygen.org/publication/PubMed/15707572" }, { "database": "PubMed", "id": "15707596", "url": "https://glygen.org/publication/PubMed/15707596" }, { "database": "PubMed", "id": "15785954", "url": "https://glygen.org/publication/PubMed/15785954" }, { "database": "PubMed", "id": "15817454", "url": "https://glygen.org/publication/PubMed/15817454" }, { "database": "PubMed", "id": "15890789", "url": "https://glygen.org/publication/PubMed/15890789" }, { "database": "PubMed", "id": "15963258", "url": "https://glygen.org/publication/PubMed/15963258" }, { "database": "PubMed", "id": "16039608", "url": "https://glygen.org/publication/PubMed/16039608" }, { "database": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" }, { "database": "PubMed", "id": "16159962", "url": "https://glygen.org/publication/PubMed/16159962" }, { "database": "PubMed", "id": "16195476", "url": "https://glygen.org/publication/PubMed/16195476" }, { "database": "PubMed", "id": "16253116", "url": "https://glygen.org/publication/PubMed/16253116" }, { "database": "PubMed", "id": "16267008", "url": "https://glygen.org/publication/PubMed/16267008" }, { "database": "PubMed", "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754" }, { "database": "PubMed", "id": "16415178", "url": "https://glygen.org/publication/PubMed/16415178" }, { "database": "PubMed", "id": "16461767", "url": "https://glygen.org/publication/PubMed/16461767" }, { "database": "PubMed", "id": "16473349", "url": "https://glygen.org/publication/PubMed/16473349" }, { "database": "PubMed", "id": "16523241", "url": "https://glygen.org/publication/PubMed/16523241" }, { "database": "PubMed", "id": "16574795", "url": "https://glygen.org/publication/PubMed/16574795" }, { "database": "PubMed", "id": "16728403", "url": "https://glygen.org/publication/PubMed/16728403" }, { "database": "PubMed", "id": "16847103", "url": "https://glygen.org/publication/PubMed/16847103" }, { "database": "PubMed", "id": "16912186", "url": "https://glygen.org/publication/PubMed/16912186" }, { "database": "PubMed", "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494" }, { "database": "PubMed", "id": "16920701", "url": "https://glygen.org/publication/PubMed/16920701" }, { "database": "PubMed", "id": "16998832", "url": "https://glygen.org/publication/PubMed/16998832" }, { "database": "PubMed", "id": "17081517", "url": "https://glygen.org/publication/PubMed/17081517" }, { "database": "PubMed", "id": "17088251", "url": "https://glygen.org/publication/PubMed/17088251" }, { "database": "PubMed", "id": "17096371", "url": "https://glygen.org/publication/PubMed/17096371" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" }, { "database": "PubMed", "id": "17215324", "url": "https://glygen.org/publication/PubMed/17215324" }, { "database": "PubMed", "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439" }, { "database": "PubMed", "id": "17234774", "url": "https://glygen.org/publication/PubMed/17234774" }, { "database": "PubMed", "id": "17234784", "url": "https://glygen.org/publication/PubMed/17234784" }, { "database": "PubMed", "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116" }, { "database": "PubMed", "id": "17395594", "url": "https://glygen.org/publication/PubMed/17395594" }, { "database": "PubMed", "id": "17431114", "url": "https://glygen.org/publication/PubMed/17431114" }, { "database": "PubMed", "id": "17497960", "url": "https://glygen.org/publication/PubMed/17497960" }, { "database": "PubMed", "id": "17524523", "url": "https://glygen.org/publication/PubMed/17524523" }, { "database": "PubMed", "id": "17721515", "url": "https://glygen.org/publication/PubMed/17721515" }, { "database": "PubMed", "id": "17898132", "url": "https://glygen.org/publication/PubMed/17898132" }, { "database": "PubMed", "id": "18006843", "url": "https://glygen.org/publication/PubMed/18006843" }, { "database": "PubMed", "id": "18032789", "url": "https://glygen.org/publication/PubMed/18032789" }, { "database": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" }, { "database": "PubMed", "id": "18198129", "url": "https://glygen.org/publication/PubMed/18198129" }, { "database": "PubMed", "id": "18314876", "url": "https://glygen.org/publication/PubMed/18314876" }, { "database": "PubMed", "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694" }, { "database": "PubMed", "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846" }, { "database": "PubMed", "id": "18382658", "url": "https://glygen.org/publication/PubMed/18382658" }, { "database": "PubMed", "id": "18562041", "url": "https://glygen.org/publication/PubMed/18562041" }, { "database": "PubMed", "id": "18676832", "url": "https://glygen.org/publication/PubMed/18676832" }, { "database": "PubMed", "id": "18757826", "url": "https://glygen.org/publication/PubMed/18757826" }, { "database": "PubMed", "id": "18774960", "url": "https://glygen.org/publication/PubMed/18774960" }, { "database": "PubMed", "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444" }, { "database": "PubMed", "id": "18922173", "url": "https://glygen.org/publication/PubMed/18922173" }, { "database": "PubMed", "id": "18923058", "url": "https://glygen.org/publication/PubMed/18923058" }, { "database": "PubMed", "id": "18930841", "url": "https://glygen.org/publication/PubMed/18930841" }, { "database": "PubMed", "id": "18989950", "url": "https://glygen.org/publication/PubMed/18989950" }, { "database": "PubMed", "id": "19029090", "url": "https://glygen.org/publication/PubMed/19029090" }, { "database": "PubMed", "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626" }, { "database": "PubMed", "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436" }, { "database": "PubMed", "id": "19260479", "url": "https://glygen.org/publication/PubMed/19260479" }, { "database": "PubMed", "id": "19294408", "url": "https://glygen.org/publication/PubMed/19294408" }, { "database": "PubMed", "id": "19297531", "url": "https://glygen.org/publication/PubMed/19297531" }, { "database": "PubMed", "id": "19553453", "url": "https://glygen.org/publication/PubMed/19553453" }, { "database": "PubMed", "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240" }, { "database": "PubMed", "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053" }, { "database": "PubMed", "id": "19671193", "url": "https://glygen.org/publication/PubMed/19671193" }, { "database": "PubMed", "id": "19695571", "url": "https://glygen.org/publication/PubMed/19695571" }, { "database": "PubMed", "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433" }, { "database": "PubMed", "id": "19787193", "url": "https://glygen.org/publication/PubMed/19787193" }, { "database": "PubMed", "id": "19826415", "url": "https://glygen.org/publication/PubMed/19826415" }, { "database": "PubMed", "id": "19834610", "url": "https://glygen.org/publication/PubMed/19834610" }, { "database": "PubMed", "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375" }, { "database": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" }, { "database": "PubMed", "id": "19931412", "url": "https://glygen.org/publication/PubMed/19931412" }, { "database": "PubMed", "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455" }, { "database": "PubMed", "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849" }, { "database": "PubMed", "id": "20021699", "url": "https://glygen.org/publication/PubMed/20021699" }, { "database": "PubMed", "id": "20082722", "url": "https://glygen.org/publication/PubMed/20082722" }, { "database": "PubMed", "id": "20122724", "url": "https://glygen.org/publication/PubMed/20122724" }, { "database": "PubMed", "id": "20160475", "url": "https://glygen.org/publication/PubMed/20160475" }, { "database": "PubMed", "id": "20180147", "url": "https://glygen.org/publication/PubMed/20180147" }, { "database": "PubMed", "id": "20224789", "url": "https://glygen.org/publication/PubMed/20224789" }, { "database": "PubMed", "id": "20308429", "url": "https://glygen.org/publication/PubMed/20308429" }, { "database": "PubMed", "id": "20354780", "url": "https://glygen.org/publication/PubMed/20354780" }, { "database": "PubMed", "id": "20357007", "url": "https://glygen.org/publication/PubMed/20357007" }, { "database": "PubMed", "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826" }, { "database": "PubMed", "id": "20527022", "url": "https://glygen.org/publication/PubMed/20527022" }, { "database": "PubMed", "id": "20621036", "url": "https://glygen.org/publication/PubMed/20621036" }, { "database": "PubMed", "id": "20657775", "url": "https://glygen.org/publication/PubMed/20657775" }, { "database": "PubMed", "id": "20713357", "url": "https://glygen.org/publication/PubMed/20713357" }, { "database": "PubMed", "id": "20724588", "url": "https://glygen.org/publication/PubMed/20724588" }, { "database": "PubMed", "id": "20802517", "url": "https://glygen.org/publication/PubMed/20802517" }, { "database": "PubMed", "id": "20847951", "url": "https://glygen.org/publication/PubMed/20847951" }, { "database": "PubMed", "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395" }, { "database": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" }, { "database": "PubMed", "id": "21073482", "url": "https://glygen.org/publication/PubMed/21073482" }, { "database": "PubMed", "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641" }, { "database": "PubMed", "id": "21119598", "url": "https://glygen.org/publication/PubMed/21119598" }, { "database": "PubMed", "id": "21209368", "url": "https://glygen.org/publication/PubMed/21209368" }, { "database": "PubMed", "id": "21344482", "url": "https://glygen.org/publication/PubMed/21344482" }, { "database": "PubMed", "id": "21359179", "url": "https://glygen.org/publication/PubMed/21359179" }, { "database": "PubMed", "id": "21401419", "url": "https://glygen.org/publication/PubMed/21401419" }, { "database": "PubMed", "id": "21408150", "url": "https://glygen.org/publication/PubMed/21408150" }, { "database": "PubMed", "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517" }, { "database": "PubMed", "id": "21426305", "url": "https://glygen.org/publication/PubMed/21426305" }, { "database": "PubMed", "id": "21556755", "url": "https://glygen.org/publication/PubMed/21556755" }, { "database": "PubMed", "id": "21660950", "url": "https://glygen.org/publication/PubMed/21660950" }, { "database": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" }, { "database": "PubMed", "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547" }, { "database": "PubMed", "id": "21887232", "url": "https://glygen.org/publication/PubMed/21887232" }, { "database": "PubMed", "id": "21898412", "url": "https://glygen.org/publication/PubMed/21898412" }, { "database": "PubMed", "id": "21903606", "url": "https://glygen.org/publication/PubMed/21903606" }, { "database": "PubMed", "id": "21967109", "url": "https://glygen.org/publication/PubMed/21967109" }, { "database": "PubMed", "id": "22042621", "url": "https://glygen.org/publication/PubMed/22042621" }, { "database": "PubMed", "id": "22069492", "url": "https://glygen.org/publication/PubMed/22069492" }, { "database": "PubMed", "id": "22070920", "url": "https://glygen.org/publication/PubMed/22070920" }, { "database": "PubMed", "id": "22078467", "url": "https://glygen.org/publication/PubMed/22078467" }, { "database": "PubMed", "id": "22136719", "url": "https://glygen.org/publication/PubMed/22136719" }, { "database": "PubMed", "id": "22149259", "url": "https://glygen.org/publication/PubMed/22149259" }, { "database": "PubMed", "id": "22174684", "url": "https://glygen.org/publication/PubMed/22174684" }, { "database": "PubMed", "id": "22194972", "url": "https://glygen.org/publication/PubMed/22194972" }, { "database": "PubMed", "id": "22216254", "url": "https://glygen.org/publication/PubMed/22216254" }, { "database": "PubMed", "id": "22267972", "url": "https://glygen.org/publication/PubMed/22267972" }, { "database": "PubMed", "id": "22270917", "url": "https://glygen.org/publication/PubMed/22270917" }, { "database": "PubMed", "id": "22319618", "url": "https://glygen.org/publication/PubMed/22319618" }, { "database": "PubMed", "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741" }, { "database": "PubMed", "id": "22550026", "url": "https://glygen.org/publication/PubMed/22550026" }, { "database": "PubMed", "id": "22641287", "url": "https://glygen.org/publication/PubMed/22641287" }, { "database": "PubMed", "id": "22710722", "url": "https://glygen.org/publication/PubMed/22710722" }, { "database": "PubMed", "id": "22734001", "url": "https://glygen.org/publication/PubMed/22734001" }, { "database": "PubMed", "id": "22766511", "url": "https://glygen.org/publication/PubMed/22766511" }, { "database": "PubMed", "id": "22810307", "url": "https://glygen.org/publication/PubMed/22810307" }, { "database": "PubMed", "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793" }, { "database": "PubMed", "id": "22876288", "url": "https://glygen.org/publication/PubMed/22876288" }, { "database": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" }, { "database": "PubMed", "id": "22952866", "url": "https://glygen.org/publication/PubMed/22952866" }, { "database": "PubMed", "id": "22982417", "url": "https://glygen.org/publication/PubMed/22982417" }, { "database": "PubMed", "id": "23102268", "url": "https://glygen.org/publication/PubMed/23102268" }, { "database": "PubMed", "id": "23109808", "url": "https://glygen.org/publication/PubMed/23109808" }, { "database": "PubMed", "id": "23128389", "url": "https://glygen.org/publication/PubMed/23128389" }, { "database": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" }, { "database": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" }, { "database": "PubMed", "id": "23272972", "url": "https://glygen.org/publication/PubMed/23272972" }, { "database": "PubMed", "id": "23339185", "url": "https://glygen.org/publication/PubMed/23339185" }, { "database": "PubMed", "id": "23357870", "url": "https://glygen.org/publication/PubMed/23357870" }, { "database": "PubMed", "id": "23485561", "url": "https://glygen.org/publication/PubMed/23485561" }, { "database": "PubMed", "id": "23515360", "url": "https://glygen.org/publication/PubMed/23515360" }, { "database": "PubMed", "id": "23525457", "url": "https://glygen.org/publication/PubMed/23525457" }, { "database": "PubMed", "id": "23681745", "url": "https://glygen.org/publication/PubMed/23681745" }, { "database": "PubMed", "id": "23755096", "url": "https://glygen.org/publication/PubMed/23755096" }, { "database": "PubMed", "id": "23755149", "url": "https://glygen.org/publication/PubMed/23755149" }, { "database": "PubMed", "id": "23792569", "url": "https://glygen.org/publication/PubMed/23792569" }, { "database": "PubMed", "id": "23812425", "url": "https://glygen.org/publication/PubMed/23812425" }, { "database": "PubMed", "id": "23836527", "url": "https://glygen.org/publication/PubMed/23836527" }, { "database": "PubMed", "id": "23858760", "url": "https://glygen.org/publication/PubMed/23858760" }, { "database": "PubMed", "id": "23874694", "url": "https://glygen.org/publication/PubMed/23874694" }, { "database": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" }, { "database": "PubMed", "id": "23984323", "url": "https://glygen.org/publication/PubMed/23984323" }, { "database": "PubMed", "id": "24010829", "url": "https://glygen.org/publication/PubMed/24010829" }, { "database": "PubMed", "id": "24025096", "url": "https://glygen.org/publication/PubMed/24025096" }, { "database": "PubMed", "id": "24039840", "url": "https://glygen.org/publication/PubMed/24039840" }, { "database": "PubMed", "id": "24039841", "url": "https://glygen.org/publication/PubMed/24039841" }, { "database": "PubMed", "id": "24040310", "url": "https://glygen.org/publication/PubMed/24040310" }, { "database": "PubMed", "id": "24058594", "url": "https://glygen.org/publication/PubMed/24058594" }, { "database": "PubMed", "id": "24062525", "url": "https://glygen.org/publication/PubMed/24062525" }, { "database": "PubMed", "id": "24083092", "url": "https://glygen.org/publication/PubMed/24083092" }, { "database": "PubMed", "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658" }, { "database": "PubMed", "id": "24121667", "url": "https://glygen.org/publication/PubMed/24121667" }, { "database": "PubMed", "id": "24123071", "url": "https://glygen.org/publication/PubMed/24123071" }, { "database": "PubMed", "id": "24194567", "url": "https://glygen.org/publication/PubMed/24194567" }, { "database": "PubMed", "id": "24201748", "url": "https://glygen.org/publication/PubMed/24201748" }, { "database": "PubMed", "id": "24260201", "url": "https://glygen.org/publication/PubMed/24260201" }, { "database": "PubMed", "id": "24290759", "url": "https://glygen.org/publication/PubMed/24290759" }, { "database": "PubMed", "id": "24294595", "url": "https://glygen.org/publication/PubMed/24294595" }, { "database": "PubMed", "id": "24360952", "url": "https://glygen.org/publication/PubMed/24360952" }, { "database": "PubMed", "id": "24370784", "url": "https://glygen.org/publication/PubMed/24370784" }, { "database": "PubMed", "id": "24381802", "url": "https://glygen.org/publication/PubMed/24381802" }, { "database": "PubMed", "id": "24409152", "url": "https://glygen.org/publication/PubMed/24409152" }, { "database": "PubMed", "id": "24533083", "url": "https://glygen.org/publication/PubMed/24533083" }, { "database": "PubMed", "id": "24586773", "url": "https://glygen.org/publication/PubMed/24586773" }, { "database": "PubMed", "id": "24632806", "url": "https://glygen.org/publication/PubMed/24632806" }, { "database": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" }, { "database": "PubMed", "id": "24655477", "url": "https://glygen.org/publication/PubMed/24655477" }, { "database": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" }, { "database": "PubMed", "id": "24706070", "url": "https://glygen.org/publication/PubMed/24706070" }, { "database": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" }, { "database": "PubMed", "id": "24772088", "url": "https://glygen.org/publication/PubMed/24772088" }, { "database": "PubMed", "id": "24786638", "url": "https://glygen.org/publication/PubMed/24786638" }, { "database": "PubMed", "id": "24858039", "url": "https://glygen.org/publication/PubMed/24858039" }, { "database": "PubMed", "id": "24863845", "url": "https://glygen.org/publication/PubMed/24863845" }, { "database": "PubMed", "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534" }, { "database": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" }, { "database": "PubMed", "id": "24894151", "url": "https://glygen.org/publication/PubMed/24894151" }, { "database": "PubMed", "id": "24911159", "url": "https://glygen.org/publication/PubMed/24911159" }, { "database": "PubMed", "id": "24999733", "url": "https://glygen.org/publication/PubMed/24999733" }, { "database": "PubMed", "id": "25056351", "url": "https://glygen.org/publication/PubMed/25056351" }, { "database": "PubMed", "id": "25113248", "url": "https://glygen.org/publication/PubMed/25113248" }, { "database": "PubMed", "id": "25187949", "url": "https://glygen.org/publication/PubMed/25187949" }, { "database": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" }, { "database": "PubMed", "id": "25226367", "url": "https://glygen.org/publication/PubMed/25226367" }, { "database": "PubMed", "id": "25277206", "url": "https://glygen.org/publication/PubMed/25277206" }, { "database": "PubMed", "id": "25300309", "url": "https://glygen.org/publication/PubMed/25300309" }, { "database": "PubMed", "id": "25313365", "url": "https://glygen.org/publication/PubMed/25313365" }, { "database": "PubMed", "id": "25351103", "url": "https://glygen.org/publication/PubMed/25351103" }, { "database": "PubMed", "id": "25428919", "url": "https://glygen.org/publication/PubMed/25428919" }, { "database": "PubMed", "id": "25486573", "url": "https://glygen.org/publication/PubMed/25486573" }, { "database": "PubMed", "id": "25539072", "url": "https://glygen.org/publication/PubMed/25539072" }, { "database": "PubMed", "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393" }, { "database": "PubMed", "id": "25617898", "url": "https://glygen.org/publication/PubMed/25617898" }, { "database": "PubMed", "id": "25631868", "url": "https://glygen.org/publication/PubMed/25631868" }, { "database": "PubMed", "id": "25705585", "url": "https://glygen.org/publication/PubMed/25705585" }, { "database": "PubMed", "id": "25708150", "url": "https://glygen.org/publication/PubMed/25708150" }, { "database": "PubMed", "id": "25749031", "url": "https://glygen.org/publication/PubMed/25749031" }, { "database": "PubMed", "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414" }, { "database": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" }, { "database": "PubMed", "id": "25868388", "url": "https://glygen.org/publication/PubMed/25868388" }, { "database": "PubMed", "id": "25880415", "url": "https://glygen.org/publication/PubMed/25880415" }, { "database": "PubMed", "id": "25889845", "url": "https://glygen.org/publication/PubMed/25889845" }, { "database": "PubMed", "id": "25890707", "url": "https://glygen.org/publication/PubMed/25890707" }, { "database": "PubMed", "id": "25947155", "url": "https://glygen.org/publication/PubMed/25947155" }, { "database": "PubMed", "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790" }, { "database": "PubMed", "id": "25958313", "url": "https://glygen.org/publication/PubMed/25958313" }, { "database": "PubMed", "id": "25978354", "url": "https://glygen.org/publication/PubMed/25978354" }, { "database": "PubMed", "id": "25980494", "url": "https://glygen.org/publication/PubMed/25980494" }, { "database": "PubMed", "id": "26004127", "url": "https://glygen.org/publication/PubMed/26004127" }, { "database": "PubMed", "id": "26079101", "url": "https://glygen.org/publication/PubMed/26079101" }, { "database": "PubMed", "id": "26110647", "url": "https://glygen.org/publication/PubMed/26110647" }, { "database": "PubMed", "id": "26119934", "url": "https://glygen.org/publication/PubMed/26119934" }, { "database": "PubMed", "id": "26172215", "url": "https://glygen.org/publication/PubMed/26172215" }, { "database": "PubMed", "id": "26216901", "url": "https://glygen.org/publication/PubMed/26216901" }, { "database": "PubMed", "id": "26230358", "url": "https://glygen.org/publication/PubMed/26230358" }, { "database": "PubMed", "id": "26245992", "url": "https://glygen.org/publication/PubMed/26245992" }, { "database": "PubMed", "id": "26294392", "url": "https://glygen.org/publication/PubMed/26294392" }, { "database": "PubMed", "id": "26300973", "url": "https://glygen.org/publication/PubMed/26300973" }, { "database": "PubMed", "id": "26365310", "url": "https://glygen.org/publication/PubMed/26365310" }, { "database": "PubMed", "id": "26375443", "url": "https://glygen.org/publication/PubMed/26375443" }, { "database": "PubMed", "id": "26377974", "url": "https://glygen.org/publication/PubMed/26377974" }, { "database": "PubMed", "id": "26393679", "url": "https://glygen.org/publication/PubMed/26393679" }, { "database": "PubMed", "id": "26406376", "url": "https://glygen.org/publication/PubMed/26406376" }, { "database": "PubMed", "id": "26456697", "url": "https://glygen.org/publication/PubMed/26456697" }, { "database": "PubMed", "id": "26501082", "url": "https://glygen.org/publication/PubMed/26501082" }, { "database": "PubMed", "id": "26542021", "url": "https://glygen.org/publication/PubMed/26542021" }, { "database": "PubMed", "id": "26546726", "url": "https://glygen.org/publication/PubMed/26546726" }, { "database": "PubMed", "id": "26549523", "url": "https://glygen.org/publication/PubMed/26549523" }, { "database": "PubMed", "id": "26556867", "url": "https://glygen.org/publication/PubMed/26556867" }, { "database": "PubMed", "id": "26649283", "url": "https://glygen.org/publication/PubMed/26649283" }, { "database": "PubMed", "id": "26689988", "url": "https://glygen.org/publication/PubMed/26689988" }, { "database": "PubMed", "id": "26700725", "url": "https://glygen.org/publication/PubMed/26700725" }, { "database": "PubMed", "id": "26703626", "url": "https://glygen.org/publication/PubMed/26703626" }, { "database": "PubMed", "id": "26751774", "url": "https://glygen.org/publication/PubMed/26751774" }, { "database": "PubMed", "id": "26752742", "url": "https://glygen.org/publication/PubMed/26752742" }, { "database": "PubMed", "id": "26788094", "url": "https://glygen.org/publication/PubMed/26788094" }, { "database": "PubMed", "id": "26821125", "url": "https://glygen.org/publication/PubMed/26821125" }, { "database": "PubMed", "id": "26833789", "url": "https://glygen.org/publication/PubMed/26833789" }, { "database": "PubMed", "id": "26842895", "url": "https://glygen.org/publication/PubMed/26842895" }, { "database": "PubMed", "id": "26848618", "url": "https://glygen.org/publication/PubMed/26848618" }, { "database": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" }, { "database": "PubMed", "id": "26893679", "url": "https://glygen.org/publication/PubMed/26893679" }, { "database": "PubMed", "id": "26931461", "url": "https://glygen.org/publication/PubMed/26931461" }, { "database": "PubMed", "id": "26961176", "url": "https://glygen.org/publication/PubMed/26961176" }, { "database": "PubMed", "id": "26975850", "url": "https://glygen.org/publication/PubMed/26975850" }, { "database": "PubMed", "id": "26984508", "url": "https://glygen.org/publication/PubMed/26984508" }, { "database": "PubMed", "id": "26984511", "url": "https://glygen.org/publication/PubMed/26984511" }, { "database": "PubMed", "id": "26988603", "url": "https://glygen.org/publication/PubMed/26988603" }, { "database": "PubMed", "id": "26993780", "url": "https://glygen.org/publication/PubMed/26993780" }, { "database": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" }, { "database": "PubMed", "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276" }, { "database": "PubMed", "id": "27191259", "url": "https://glygen.org/publication/PubMed/27191259" }, { "database": "PubMed", "id": "27220365", "url": "https://glygen.org/publication/PubMed/27220365" }, { "database": "PubMed", "id": "27237320", "url": "https://glygen.org/publication/PubMed/27237320" }, { "database": "PubMed", "id": "27246739", "url": "https://glygen.org/publication/PubMed/27246739" }, { "database": "PubMed", "id": "27248472", "url": "https://glygen.org/publication/PubMed/27248472" }, { "database": "PubMed", "id": "27278471", "url": "https://glygen.org/publication/PubMed/27278471" }, { "database": "PubMed", "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256" }, { "database": "PubMed", "id": "27344177", "url": "https://glygen.org/publication/PubMed/27344177" }, { "database": "PubMed", "id": "27363027", "url": "https://glygen.org/publication/PubMed/27363027" }, { "database": "PubMed", "id": "27402964", "url": "https://glygen.org/publication/PubMed/27402964" }, { "database": "PubMed", "id": "27428469", "url": "https://glygen.org/publication/PubMed/27428469" }, { "database": "PubMed", "id": "27460083", "url": "https://glygen.org/publication/PubMed/27460083" }, { "database": "PubMed", "id": "27462783", "url": "https://glygen.org/publication/PubMed/27462783" }, { "database": "PubMed", "id": "27467982", "url": "https://glygen.org/publication/PubMed/27467982" }, { "database": "PubMed", "id": "27487141", "url": "https://glygen.org/publication/PubMed/27487141" }, { "database": "PubMed", "id": "27542844", "url": "https://glygen.org/publication/PubMed/27542844" }, { "database": "PubMed", "id": "27567948", "url": "https://glygen.org/publication/PubMed/27567948" }, { "database": "PubMed", "id": "27602495", "url": "https://glygen.org/publication/PubMed/27602495" }, { "database": "PubMed", "id": "27611942", "url": "https://glygen.org/publication/PubMed/27611942" }, { "database": "PubMed", "id": "27638858", "url": "https://glygen.org/publication/PubMed/27638858" }, { "database": "PubMed", "id": "27715394", "url": "https://glygen.org/publication/PubMed/27715394" }, { "database": "PubMed", "id": "27845385", "url": "https://glygen.org/publication/PubMed/27845385" }, { "database": "PubMed", "id": "28053698", "url": "https://glygen.org/publication/PubMed/28053698" }, { "database": "PubMed", "id": "28068967", "url": "https://glygen.org/publication/PubMed/28068967" }, { "database": "PubMed", "id": "28076322", "url": "https://glygen.org/publication/PubMed/28076322" }, { "database": "PubMed", "id": "28124908", "url": "https://glygen.org/publication/PubMed/28124908" }, { "database": "PubMed", "id": "28134933", "url": "https://glygen.org/publication/PubMed/28134933" }, { "database": "PubMed", "id": "28188308", "url": "https://glygen.org/publication/PubMed/28188308" }, { "database": "PubMed", "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177" }, { "database": "PubMed", "id": "28225063", "url": "https://glygen.org/publication/PubMed/28225063" }, { "database": "PubMed", "id": "28257035", "url": "https://glygen.org/publication/PubMed/28257035" }, { "database": "PubMed", "id": "28338656", "url": "https://glygen.org/publication/PubMed/28338656" }, { "database": "PubMed", "id": "28361970", "url": "https://glygen.org/publication/PubMed/28361970" }, { "database": "PubMed", "id": "28398603", "url": "https://glygen.org/publication/PubMed/28398603" }, { "database": "PubMed", "id": "28406574", "url": "https://glygen.org/publication/PubMed/28406574" }, { "database": "PubMed", "id": "28415713", "url": "https://glygen.org/publication/PubMed/28415713" }, { "database": "PubMed", "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903" }, { "database": "PubMed", "id": "28423580", "url": "https://glygen.org/publication/PubMed/28423580" }, { "database": "PubMed", "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224" }, { "database": "PubMed", "id": "28445805", "url": "https://glygen.org/publication/PubMed/28445805" }, { "database": "PubMed", "id": "28450296", "url": "https://glygen.org/publication/PubMed/28450296" }, { "database": "PubMed", "id": "28459432", "url": "https://glygen.org/publication/PubMed/28459432" }, { "database": "PubMed", "id": "28507287", "url": "https://glygen.org/publication/PubMed/28507287" }, { "database": "PubMed", "id": "28542214", "url": "https://glygen.org/publication/PubMed/28542214" }, { "database": "PubMed", "id": "28624785", "url": "https://glygen.org/publication/PubMed/28624785" }, { "database": "PubMed", "id": "28642549", "url": "https://glygen.org/publication/PubMed/28642549" }, { "database": "PubMed", "id": "28667800", "url": "https://glygen.org/publication/PubMed/28667800" }, { "database": "PubMed", "id": "28715434", "url": "https://glygen.org/publication/PubMed/28715434" }, { "database": "PubMed", "id": "28741790", "url": "https://glygen.org/publication/PubMed/28741790" }, { "database": "PubMed", "id": "29021002", "url": "https://glygen.org/publication/PubMed/29021002" }, { "database": "PubMed", "id": "29036202", "url": "https://glygen.org/publication/PubMed/29036202" }, { "database": "PubMed", "id": "29039492", "url": "https://glygen.org/publication/PubMed/29039492" }, { "database": "PubMed", "id": "29046395", "url": "https://glygen.org/publication/PubMed/29046395" }, { "database": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" }, { "database": "PubMed", "id": "29066806", "url": "https://glygen.org/publication/PubMed/29066806" }, { "database": "PubMed", "id": "29088849", "url": "https://glygen.org/publication/PubMed/29088849" }, { "database": "PubMed", "id": "29151962", "url": "https://glygen.org/publication/PubMed/29151962" }, { "database": "PubMed", "id": "29158989", "url": "https://glygen.org/publication/PubMed/29158989" }, { "database": "PubMed", "id": "29186907", "url": "https://glygen.org/publication/PubMed/29186907" }, { "database": "PubMed", "id": "29190494", "url": "https://glygen.org/publication/PubMed/29190494" }, { "database": "PubMed", "id": "29228673", "url": "https://glygen.org/publication/PubMed/29228673" }, { "database": "PubMed", "id": "29263678", "url": "https://glygen.org/publication/PubMed/29263678" }, { "database": "PubMed", "id": "29276408", "url": "https://glygen.org/publication/PubMed/29276408" }, { "database": "PubMed", "id": "29311227", "url": "https://glygen.org/publication/PubMed/29311227" }, { "database": "PubMed", "id": "29382358", "url": "https://glygen.org/publication/PubMed/29382358" }, { "database": "PubMed", "id": "29422613", "url": "https://glygen.org/publication/PubMed/29422613" }, { "database": "PubMed", "id": "29434841", "url": "https://glygen.org/publication/PubMed/29434841" }, { "database": "PubMed", "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667" }, { "database": "PubMed", "id": "29484384", "url": "https://glygen.org/publication/PubMed/29484384" }, { "database": "PubMed", "id": "29491429", "url": "https://glygen.org/publication/PubMed/29491429" }, { "database": "PubMed", "id": "29535802", "url": "https://glygen.org/publication/PubMed/29535802" }, { "database": "PubMed", "id": "29563383", "url": "https://glygen.org/publication/PubMed/29563383" }, { "database": "PubMed", "id": "29593542", "url": "https://glygen.org/publication/PubMed/29593542" }, { "database": "PubMed", "id": "29700289", "url": "https://glygen.org/publication/PubMed/29700289" }, { "database": "PubMed", "id": "29728077", "url": "https://glygen.org/publication/PubMed/29728077" }, { "database": "PubMed", "id": "29740072", "url": "https://glygen.org/publication/PubMed/29740072" }, { "database": "PubMed", "id": "29752441", "url": "https://glygen.org/publication/PubMed/29752441" }, { "database": "PubMed", "id": "29791208", "url": "https://glygen.org/publication/PubMed/29791208" }, { "database": "PubMed", "id": "29796177", "url": "https://glygen.org/publication/PubMed/29796177" }, { "database": "PubMed", "id": "29903032", "url": "https://glygen.org/publication/PubMed/29903032" }, { "database": "PubMed", "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029" }, { "database": "PubMed", "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374" }, { "database": "PubMed", "id": "29986550", "url": "https://glygen.org/publication/PubMed/29986550" }, { "database": "PubMed", "id": "29993014", "url": "https://glygen.org/publication/PubMed/29993014" }, { "database": "PubMed", "id": "30013514", "url": "https://glygen.org/publication/PubMed/30013514" }, { "database": "PubMed", "id": "30033448", "url": "https://glygen.org/publication/PubMed/30033448" }, { "database": "PubMed", "id": "30055645", "url": "https://glygen.org/publication/PubMed/30055645" }, { "database": "PubMed", "id": "30065198", "url": "https://glygen.org/publication/PubMed/30065198" }, { "database": "PubMed", "id": "30087707", "url": "https://glygen.org/publication/PubMed/30087707" }, { "database": "PubMed", "id": "30166526", "url": "https://glygen.org/publication/PubMed/30166526" }, { "database": "PubMed", "id": "30332774", "url": "https://glygen.org/publication/PubMed/30332774" }, { "database": "PubMed", "id": "30337877", "url": "https://glygen.org/publication/PubMed/30337877" }, { "database": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" }, { "database": "PubMed", "id": "30387148", "url": "https://glygen.org/publication/PubMed/30387148" }, { "database": "PubMed", "id": "30458784", "url": "https://glygen.org/publication/PubMed/30458784" }, { "database": "PubMed", "id": "30464516", "url": "https://glygen.org/publication/PubMed/30464516" }, { "database": "PubMed", "id": "30488595", "url": "https://glygen.org/publication/PubMed/30488595" }, { "database": "PubMed", "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362" }, { "database": "PubMed", "id": "30531837", "url": "https://glygen.org/publication/PubMed/30531837" }, { "database": "PubMed", "id": "30539198", "url": "https://glygen.org/publication/PubMed/30539198" }, { "database": "PubMed", "id": "30555628", "url": "https://glygen.org/publication/PubMed/30555628" }, { "database": "PubMed", "id": "30563275", "url": "https://glygen.org/publication/PubMed/30563275" }, { "database": "PubMed", "id": "30571746", "url": "https://glygen.org/publication/PubMed/30571746" }, { "database": "PubMed", "id": "30696915", "url": "https://glygen.org/publication/PubMed/30696915" }, { "database": "PubMed", "id": "30717801", "url": "https://glygen.org/publication/PubMed/30717801" }, { "database": "PubMed", "id": "30728047", "url": "https://glygen.org/publication/PubMed/30728047" }, { "database": "PubMed", "id": "30742951", "url": "https://glygen.org/publication/PubMed/30742951" }, { "database": "PubMed", "id": "30744493", "url": "https://glygen.org/publication/PubMed/30744493" }, { "database": "PubMed", "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269" }, { "database": "PubMed", "id": "30779783", "url": "https://glygen.org/publication/PubMed/30779783" }, { "database": "PubMed", "id": "30816469", "url": "https://glygen.org/publication/PubMed/30816469" }, { "database": "PubMed", "id": "30836148", "url": "https://glygen.org/publication/PubMed/30836148" }, { "database": "PubMed", "id": "30894654", "url": "https://glygen.org/publication/PubMed/30894654" }, { "database": "PubMed", "id": "30920523", "url": "https://glygen.org/publication/PubMed/30920523" }, { "database": "PubMed", "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845" }, { "database": "PubMed", "id": "31060904", "url": "https://glygen.org/publication/PubMed/31060904" }, { "database": "PubMed", "id": "31160603", "url": "https://glygen.org/publication/PubMed/31160603" }, { "database": "PubMed", "id": "31170089", "url": "https://glygen.org/publication/PubMed/31170089" }, { "database": "PubMed", "id": "31186741", "url": "https://glygen.org/publication/PubMed/31186741" }, { "database": "PubMed", "id": "31297342", "url": "https://glygen.org/publication/PubMed/31297342" }, { "database": "PubMed", "id": "31383893", "url": "https://glygen.org/publication/PubMed/31383893" }, { "database": "PubMed", "id": "31420553", "url": "https://glygen.org/publication/PubMed/31420553" }, { "database": "PubMed", "id": "31428520", "url": "https://glygen.org/publication/PubMed/31428520" }, { "database": "PubMed", "id": "31478830", "url": "https://glygen.org/publication/PubMed/31478830" }, { "database": "PubMed", "id": "31480645", "url": "https://glygen.org/publication/PubMed/31480645" }, { "database": "PubMed", "id": "31501460", "url": "https://glygen.org/publication/PubMed/31501460" }, { "database": "PubMed", "id": "31516757", "url": "https://glygen.org/publication/PubMed/31516757" }, { "database": "PubMed", "id": "31519958", "url": "https://glygen.org/publication/PubMed/31519958" }, { "database": "PubMed", "id": "31554180", "url": "https://glygen.org/publication/PubMed/31554180" }, { "database": "PubMed", "id": "31565187", "url": "https://glygen.org/publication/PubMed/31565187" }, { "database": "PubMed", "id": "31627430", "url": "https://glygen.org/publication/PubMed/31627430" }, { "database": "PubMed", "id": "31648990", "url": "https://glygen.org/publication/PubMed/31648990" }, { "database": "PubMed", "id": "31652779", "url": "https://glygen.org/publication/PubMed/31652779" }, { "database": "PubMed", "id": "31654241", "url": "https://glygen.org/publication/PubMed/31654241" }, { "database": "PubMed", "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408" }, { "database": "PubMed", "id": "31671889", "url": "https://glygen.org/publication/PubMed/31671889" }, { "database": "PubMed", "id": "31831830", "url": "https://glygen.org/publication/PubMed/31831830" }, { "database": "PubMed", "id": "31867162", "url": "https://glygen.org/publication/PubMed/31867162" }, { "database": "PubMed", "id": "31870092", "url": "https://glygen.org/publication/PubMed/31870092" }, { "database": "PubMed", "id": "31926619", "url": "https://glygen.org/publication/PubMed/31926619" }, { "database": "PubMed", "id": "32155953", "url": "https://glygen.org/publication/PubMed/32155953" }, { "database": "PubMed", "id": "32256987", "url": "https://glygen.org/publication/PubMed/32256987" }, { "database": "PubMed", "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611" }, { "database": "PubMed", "id": "32286266", "url": "https://glygen.org/publication/PubMed/32286266" }, { "database": "PubMed", "id": "32337793", "url": "https://glygen.org/publication/PubMed/32337793" }, { "database": "PubMed", "id": "32415208", "url": "https://glygen.org/publication/PubMed/32415208" }, { "database": "PubMed", "id": "32604782", "url": "https://glygen.org/publication/PubMed/32604782" }, { "database": "PubMed", "id": "32733919", "url": "https://glygen.org/publication/PubMed/32733919" }, { "database": "PubMed", "id": "32784087", "url": "https://glygen.org/publication/PubMed/32784087" }, { "database": "PubMed", "id": "32806748", "url": "https://glygen.org/publication/PubMed/32806748" }, { "database": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" }, { "database": "PubMed", "id": "32844749", "url": "https://glygen.org/publication/PubMed/32844749" }, { "database": "PubMed", "id": "32848136", "url": "https://glygen.org/publication/PubMed/32848136" }, { "database": "PubMed", "id": "32850845", "url": "https://glygen.org/publication/PubMed/32850845" }, { "database": "PubMed", "id": "32872257", "url": "https://glygen.org/publication/PubMed/32872257" }, { "database": "PubMed", "id": "33025708", "url": "https://glygen.org/publication/PubMed/33025708" }, { "database": "PubMed", "id": "33036231", "url": "https://glygen.org/publication/PubMed/33036231" }, { "database": "PubMed", "id": "33076263", "url": "https://glygen.org/publication/PubMed/33076263" }, { "database": "PubMed", "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263" }, { "database": "PubMed", "id": "33287873", "url": "https://glygen.org/publication/PubMed/33287873" }, { "database": "PubMed", "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438" }, { "database": "PubMed", "id": "33420364", "url": "https://glygen.org/publication/PubMed/33420364" }, { "database": "PubMed", "id": "33532186", "url": "https://glygen.org/publication/PubMed/33532186" }, { "database": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" }, { "database": "PubMed", "id": "33634070", "url": "https://glygen.org/publication/PubMed/33634070" }, { "database": "PubMed", "id": "33668531", "url": "https://glygen.org/publication/PubMed/33668531" }, { "database": "PubMed", "id": "33715263", "url": "https://glygen.org/publication/PubMed/33715263" }, { "database": "PubMed", "id": "33724150", "url": "https://glygen.org/publication/PubMed/33724150" }, { "database": "PubMed", "id": "33750427", "url": "https://glygen.org/publication/PubMed/33750427" }, { "database": "PubMed", "id": "33799345", "url": "https://glygen.org/publication/PubMed/33799345" }, { "database": "PubMed", "id": "33846818", "url": "https://glygen.org/publication/PubMed/33846818" }, { "database": "PubMed", "id": "33898431", "url": "https://glygen.org/publication/PubMed/33898431" }, { "database": "PubMed", "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284" }, { "database": "PubMed", "id": "33981002", "url": "https://glygen.org/publication/PubMed/33981002" }, { "database": "PubMed", "id": "35201437", "url": "https://glygen.org/publication/PubMed/35201437" }, { "database": "PubMed", "id": "35257717", "url": "https://glygen.org/publication/PubMed/35257717" }, { "database": "PubMed", "id": "35426066", "url": "https://glygen.org/publication/PubMed/35426066" }, { "database": "PubMed", "id": "35962191", "url": "https://glygen.org/publication/PubMed/35962191" }, { "database": "PubMed", "id": "35982848", "url": "https://glygen.org/publication/PubMed/35982848" }, { "database": "PubMed", "id": "36009384", "url": "https://glygen.org/publication/PubMed/36009384" }, { "database": "PubMed", "id": "7553664", "url": "https://glygen.org/publication/PubMed/7553664" }, { "database": "PubMed", "id": "7739563", "url": "https://glygen.org/publication/PubMed/7739563" }, { "database": "PubMed", "id": "8051157", "url": "https://glygen.org/publication/PubMed/8051157" }, { "database": "PubMed", "id": "8824286", "url": "https://glygen.org/publication/PubMed/8824286" }, { "database": "PubMed", "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336" }, { "database": "PubMed", "id": "9148935", "url": "https://glygen.org/publication/PubMed/9148935" }, { "database": "PubMed", "id": "9416004", "url": "https://glygen.org/publication/PubMed/9416004" }, { "database": "PubMed", "id": "9922457", "url": "https://glygen.org/publication/PubMed/9922457" }, { "database": "PubMed", "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ], "site_lbl": "Tyr397" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q05397-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05397-1.386.386", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q05397-1.390.390", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.407.407", "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": 6 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 537 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.928.928", "start_pos": 928, "end_pos": 928, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Interaction of Hic-5, A senescence-related protein, with focal adhesion kinase.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Fujita H, Kamiguchi K, Cho D, Shibanuma M, Morimoto C, Tachibana K", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9756887", "url": "https://glygen.org/publication/PubMed/9756887" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "9756887", "url": "https://glygen.org/publication/PubMed/9756887", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EISPPPTANLDRSNDKVYEN", "down_seq": "TGLVKAVIEMSSKIQPAPPE", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "G", "comment": "Loss of interaction with TGFB1I1.", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "9756887", "url": "https://glygen.org/publication/PubMed/9756887" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q05397-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q05397-1.914.914", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05397-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q05397-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q05397-1.925.925", "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": "Q05397-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VREKYELAHPPEEWKYELRI", "down_seq": "YLPKGFLNQFTEDKPTLNFF", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "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 (4).", "chr_id": "8", "chr_pos": "140864383", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R127", "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: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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q05397-1.147.147", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "RYLPKGFLNQFTEDKPTLNF", "down_seq": "YQQVKSDYMLEIADQVDQEI", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFF->NFC).", "chr_id": "8", "chr_pos": "140864322", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F147", "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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q05397-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q05397-1.148.148", "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": "Q05397-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "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": "MAAAYLDPNLNHTPN", "down_seq": "STKTHLGTGMERSPGAMERV", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "8", "chr_pos": "140890691", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S16", "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: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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser16" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05397-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q05397-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q05397-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q05397-1.29.29", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_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": "Q05397-1.17.17", "start_pos": 17, "end_pos": 17, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs746193983", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746193983", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746193983", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746193983", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746193983", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746193983#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746193983", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746193983", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MAAAYLDPNLNHTPNS", "down_seq": "TKTHLGTGMERSPGAMERVL", "snv": [ { "evidence": [ { "id": "rs746193983", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746193983" }, { "id": "rs746193983", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746193983" }, { "id": "rs746193983", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746193983#frequency_tab" }, { "id": "rs746193983", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746193983" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSI).", "chr_id": "8", "chr_pos": "140890688", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S17", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746193983", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746193983" }, { "id": "rs746193983", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746193983" }, { "id": "rs746193983", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746193983#frequency_tab" }, { "id": "rs746193983", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746193983" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NSS->NSN).", "chr_id": "8", "chr_pos": "140890688", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S17", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q05397-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q05397-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q05397-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q05397-1.29.29", "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": "Q05397-1.255.255", "start_pos": 255, "end_pos": 255, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2100052053", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100052053", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2100052053", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2100052053#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2100052053", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2100052053", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NREESILKFFEILSPVYRFD", "down_seq": "ECFKCALGSSWIISVELAIG", "snv": [ { "evidence": [ { "id": "rs2100052053", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100052053" }, { "id": "rs2100052053", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2100052053#frequency_tab" }, { "id": "rs2100052053", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2100052053" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KEC->NEC).", "chr_id": "8", "chr_pos": "140735400", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K255", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q05397-1.286.286", "start_pos": 286, "end_pos": 286, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1297792567", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1297792567", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1297792567", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1297792567", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "WIISVELAIGPEEGISYLTD", "down_seq": "GCNPTHLADFTQVQTIQYSN", "snv": [ { "evidence": [ { "id": "rs1297792567", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1297792567" }, { "id": "rs1297792567", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1297792567" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KGC->NGC).", "chr_id": "8", "chr_pos": "140818286", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K286", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q05397-1.290.290", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.290.290", "start_pos": 290, "end_pos": 290, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2100096593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100096593", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2100096593", "url": "https://www.ensembl.org/id/rs2100096593", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VELAIGPEEGISYLTDKGCN", "down_seq": "THLADFTQVQTIQYSNSEDK", "snv": [ { "evidence": [ { "id": "rs2100096593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100096593" }, { "id": "rs2100096593", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2100096593" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPT->NRT).", "chr_id": "8", "chr_pos": "140803649", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P290", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q05397-1.286.286", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.337.337", "start_pos": 337, "end_pos": 337, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QLKIAGAPEPLTVTAPSLTI", "down_seq": "ENMADLIDGYCRLVNGTSQS", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "140800542", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A337", "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: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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q05397-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.347.347", "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": "Q05397-1.341.341", "start_pos": 341, "end_pos": 341, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2100094395", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100094395", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2100094395", "url": "https://www.ensembl.org/id/rs2100094395", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AGAPEPLTVTAPSLTIAENM", "down_seq": "DLIDGYCRLVNGTSQSFIIR", "snv": [ { "evidence": [ { "id": "rs2100094395", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2100094395" }, { "id": "rs2100094395", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2100094395" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NMA->NMT).", "chr_id": "8", "chr_pos": "140800531", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A341", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q05397-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q05397-1.347.347", "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": "Q05397-1.363.363", "start_pos": 363, "end_pos": 363, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LIDGYCRLVNGTSQSFIIRP", "down_seq": "KEGERALPSIPKLANSEKQG", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "12", "frequency": "0.3", "sequence_org": "Q", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: patient count (12/4484).", "chr_id": "8", "chr_pos": "140800465", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "Q363", "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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.347.347", "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": "Q05397-1.385.385", "start_pos": 385, "end_pos": 385, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EGERALPSIPKLANSEKQGM", "down_seq": "THAVSVSETDDYAEIIDEED", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "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": "8", "chr_pos": "140789498", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R385", "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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q05397-1.386.386", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q05397-1.390.390", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q05397-1.397.397", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1798536575", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1798536575", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1798536575", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1798536575", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GMERSPGAMERVLKVFHYFE", "down_seq": "NSEPTTWASIIRHGDATDVR", "snv": [ { "evidence": [ { "id": "rs1798536575", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1798536575" }, { "id": "rs1798536575", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1798536575" } ], "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": "8", "chr_pos": "140890604", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S45", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q05397-1.54.54", "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": "Q05397-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IYMSPENPALAVAIKTCKNC", "down_seq": "SDSVREKFLQEALTMRQFDH", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NCT->NCI).", "chr_id": "8", "chr_pos": "140752270", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T460", "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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q05397-1.441.441", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q05397-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q05397-1.474.474", "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": "Q05397-1.634.634", "start_pos": 634, "end_pos": 634, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EILMHGVKPFQGVKNNDVIG", "down_seq": "IENGERLPMPPNCPPTLYSL", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "8", "chr_pos": "140735380", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R634", "disease": [ { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID: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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q05397-1.648.648", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.648.648", "start_pos": 648, "end_pos": 648, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "NNDVIGRIENGERLPMPPNC", "down_seq": "PTLYSLMTKCWAYDPSRRPR", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "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 (NCP->NCS).", "chr_id": "8", "chr_pos": "140735339", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P648", "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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q05397-1.634.634", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.767.767", "start_pos": 767, "end_pos": 767, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "YPGSHGITAMAGSIYPGQAS", "down_seq": "LDQTDSWNHRPQEIAMWQPN", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "140702638", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "L767", "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: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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q05397-1.779.779", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.779.779", "start_pos": 779, "end_pos": 779, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SIYPGQASLLDQTDSWNHRP", "down_seq": "EIAMWQPNVEDSTVLDLRGI", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "140702602", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q779", "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: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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q05397-1.767.767", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.790.790", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.790.790", "start_pos": 790, "end_pos": 790, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs763543656", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763543656", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs763543656", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763543656", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs763543656", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763543656#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs763543656", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763543656", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QTDSWNHRPQEIAMWQPNVE", "down_seq": "STVLDLRGIGQVLPTHLMEE", "snv": [ { "evidence": [ { "id": "rs763543656", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763543656" }, { "id": "rs763543656", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs763543656" }, { "id": "rs763543656", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs763543656#frequency_tab" }, { "id": "rs763543656", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs763543656" } ], "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": "8", "chr_pos": "140701022", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D790", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q05397-1.779.779", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q05397-1.824.824", "start_pos": 824, "end_pos": 824, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PTHLMEERLIRQQQEMEEDQ", "down_seq": "WLEKEERFLKPDVRLSRGSI", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "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": "8", "chr_pos": "140700920", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R824", "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": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q05397-1.840.840", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q05397-1.843.843", "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": "Q05397-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GIIQKIVDSHKVKHVACYGF", "down_seq": "LSHLRSEEVHWLHVDMGVSS", "snv": [ { "evidence": [ { "id": "Q05397", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q05397" } ], "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": "8", "chr_pos": "140879577", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R86", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "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": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q05397-1.918.918", "start_pos": 918, "end_pos": 918, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2093620866", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2093620866", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2093620866", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2093620866#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "YNEGVKLQPQEISPPPTANL", "down_seq": "RSNDKVYENVTGLVKAVIEM", "snv": [ { "evidence": [ { "id": "rs2093620866", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2093620866" }, { "id": "rs2093620866", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2093620866#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRS->NRS).", "chr_id": "8", "chr_pos": "140668382", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D918", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q05397-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q05397-1.914.914", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q05397-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q05397-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.928.928", "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": "Q05397-1.923.923", "start_pos": 923, "end_pos": 923, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2093594438", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2093594438", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2093594438", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2093594438", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KLQPQEISPPPTANLDRSND", "down_seq": "VYENVTGLVKAVIEMSSKIQ", "snv": [ { "evidence": [ { "id": "rs2093594438", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2093594438" }, { "id": "rs2093594438", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2093594438" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDK->NDT).", "chr_id": "8", "chr_pos": "140668366", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K923", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q05397-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q05397-1.914.914", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q05397-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q05397-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q05397-1.928.928", "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": "Q05397-1.1007.1007", "start_pos": 1007, "end_pos": 1007, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QKLLNSDLGELINKMKLAQQ", "down_seq": "VMTSLQQEYKKQMLTAAHAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ], "site_lbl": "Tyr1007" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q05397-1.1016.1016", "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": "Q05397-1.1016.1016", "start_pos": 1016, "end_pos": 1016, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.", "journal": "Cell", "date": "2007", "authors": "Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ELINKMKLAQQYVMTSLQQE", "down_seq": "KKQMLTAAHALAVDAKNLLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ], "site_lbl": "Tyr1016" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q05397-1.1007.1007", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q05397-1.1034.1034", "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": "Q05397-1.13.13", "start_pos": 13, "end_pos": 13, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MAAAYLDPNLNH", "down_seq": "PNSSTKTHLGTGMERSPGAM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "site_lbl": "Thr13" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q05397-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q05397-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q05397-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.29.29", "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": "Q05397-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "YLPKGFLNQFTEDKPTLNFF", "down_seq": "QQVKSDYMLEIADQVDQEIA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ], "site_lbl": "Tyr148" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q05397-1.147.147", "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": "Q05397-1.194.194", "start_pos": 194, "end_pos": 194, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of focal adhesion kinase on tyrosine 194 by Met leads to its activation through relief of autoinhibition.", "journal": "Oncogene", "date": "2011", "authors": "Chen TH, Chan PC, Chen CL, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ] }, { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LEIRRSYWEMRGNALEKKSN", "down_seq": "EVLEKDVGLKRFFPKSLLDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00533-1", "kinase_gene_name": "EGFR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr194" }, { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr194" }, { "kinase_uniprot_canonical_ac": "P09619-1", "kinase_gene_name": "PDGFRB", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr194" }, { "kinase_uniprot_canonical_ac": "P16234-1", "kinase_gene_name": "PDGFRA", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr194" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr194" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": 5 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q05397-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Inhibition of focal adhesion kinase induces apoptosis in bladder cancer cells via Src and the phosphatidylinositol 3-kinase/Akt pathway.", "journal": "Experimental and therapeutic medicine", "date": "2015", "authors": "Kong D, Chen F, Sima NI", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26640543", "url": "https://glygen.org/publication/PubMed/26640543" } ] }, { "title": "Circular RNA circPICALM sponges miR-1265 to inhibit bladder cancer metastasis and influence FAK phosphorylation.", "journal": "EBioMedicine", "date": "2019", "authors": "Yan D, Dong W, He Q, Yang M, Huang L, Kong J, Qin H, Lin T, Huang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31648990", "url": "https://glygen.org/publication/PubMed/31648990" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26640543", "url": "https://glygen.org/publication/PubMed/26640543", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31648990", "url": "https://glygen.org/publication/PubMed/31648990", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AYLDPNLNHTPNSSTKTHLG", "down_seq": "GMERSPGAMERVLKVFHYFE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "26640543", "url": "https://glygen.org/publication/PubMed/26640543" }, { "database": "PubMed", "id": "31648990", "url": "https://glygen.org/publication/PubMed/31648990" } ], "site_lbl": "Thr24" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q05397-1.5.5", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q05397-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q05397-1.29.29", "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": "Q05397-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "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": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NLNHTPNSSTKTHLGTGMER", "down_seq": "PGAMERVLKVFHYFESNSEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ], "site_lbl": "Ser29" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q05397-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q05397-1.24.24", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.45.45", "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": "Q05397-1.347.347", "start_pos": 347, "end_pos": 347, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LTVTAPSLTIAENMADLIDG", "down_seq": "CRLVNGTSQSFIIRPQKEGE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ], "site_lbl": "Tyr347" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q05397-1.337.337", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q05397-1.341.341", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.363.363", "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": "Q05397-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GERALPSIPKLANSEKQGMR", "down_seq": "HAVSVSETDDYAEIIDEEDT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Thr386" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q05397-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q05397-1.390.390", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.397.397", "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": "Q05397-1.390.390", "start_pos": 390, "end_pos": 390, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomics analysis of protein kinases by target class-selective prefractionation and tandem mass spectrometry.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Wissing J, Jansch L, Nimtz M, Dieterich G, Hornberger R, Keri G, Wehland J, Daub H", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPSIPKLANSEKQGMRTHAV", "down_seq": "VSETDDYAEIIDEEDTYTMP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ], "site_lbl": "Ser390" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q05397-1.385.385", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q05397-1.386.386", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q05397-1.397.397", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q05397-1.407.407", "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": "Q05397-1.407.407", "start_pos": 407, "end_pos": 407, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] }, { "title": "Tyrosine phosphorylation of focal adhesion kinase at sites in the catalytic domain regulates kinase activity: a role for Src family kinases.", "journal": "Molecular and cellular biology", "date": "1995", "authors": "Calalb MB, Polte TR, Hanks SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ] }, { "title": "Identification of Src-specific phosphorylation site on focal adhesion kinase: dissection of the role of Src SH2 and catalytic functions and their consequences for tumor cell behavior.", "journal": "Cancer research", "date": "2005", "authors": "Brunton VG, Avizienyte E, Fincham VJ, Serrels B, Metcalf CA 3rd, Sawyer TK, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ] }, { "title": "Growth factors stimulate kidney proximal tubule cell migration independent of augmented tyrosine phosphorylation of focal adhesion kinase.", "journal": "Biochemical and biophysical research communications", "date": "2005", "authors": "Cao Y, Baig MR, Hamm LL, Wu K, Simon EE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ] }, { "title": "Phosphorylation of focal adhesion kinase (FAK) on Ser732 is induced by rho-dependent kinase and is essential for proline-rich tyrosine kinase-2-mediated phosphorylation of FAK on Tyr407 in response to vascular endothelial growth factor.", "journal": "Molecular biology of the cell", "date": "2006", "authors": "Le Boeuf F, Houle F, Sussman M, Huot J", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434" } ] }, { "title": "Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein.", "journal": "The Biochemical journal", "date": "2003", "authors": "Relou IA, Bax LA, van Rijn HJ, Akkerman JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ] }, { "title": "The proto-oncogene Fgr regulates cell migration and this requires its plasma membrane localization.", "journal": "Experimental cell research", "date": "2005", "authors": "Continolo S, Baruzzi A, Majeed M, Caveggion E, Fumagalli L, Lowell CA, Berton G", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106" } ] }, { "title": "Nuclear localization and apoptotic regulation of an amino-terminal domain focal adhesion kinase fragment in endothelial cells.", "journal": "Biochemical and biophysical research communications", "date": "2000", "authors": "Lobo M, Zachary I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591" } ] }, { "title": "Expression of GRP and its receptor in well-differentiated colon cancer cells correlates with the presence of focal adhesion kinase phosphorylated at tyrosines 397 and 407.", "journal": "The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society", "date": "2003", "authors": "Matkowskyj KA, Keller K, Glover S, Kornberg L, Tran-Son-Tay R, Benya RV", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12871985", "url": "https://glygen.org/publication/PubMed/12871985" } ] }, { "title": "Regulation of vascular endothelial growth factor receptor 2-mediated phosphorylation of focal adhesion kinase by heat shock protein 90 and Src kinase activities.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Le Boeuf F, Houle F, Huot J", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15247219", "url": "https://glygen.org/publication/PubMed/15247219" } ] }, { "title": "Roles played by a subset of integrin signaling molecules in cadherin-based cell-cell adhesion.", "journal": "The Journal of cell biology", "date": "2004", "authors": "Yano H, Mazaki Y, Kurokawa K, Hanks SK, Matsuda M, Sabe H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" } ] }, { "title": "The microtubule binding drug laulimalide inhibits vascular endothelial growth factor-induced human endothelial cell migration and is synergistic when combined with docetaxel (taxotere).", "journal": "Molecular pharmacology", "date": "2006", "authors": "Lu H, Murtagh J, Schwartz EL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16415178", "url": "https://glygen.org/publication/PubMed/16415178" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] }, { "title": "Abnormalities in focal adhesion complex formation, regulation, and function in human autosomal recessive polycystic kidney disease epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2010", "authors": "Israeli S, Amsler K, Zheleznova N, Wilson PD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" } ] }, { "title": "Focal adhesion kinase, a downstream mediator of Raf-1 signaling, suppresses cellular adhesion, migration, and neuroendocrine markers in BON carcinoid cells.", "journal": "Molecular cancer research : MCR", "date": "2010-05", "authors": "Ning Li, Chen Herbert, Kunnimalaiyaan Muthusamy", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20407018", "url": "https://glygen.org/publication/PubMed/20407018" } ] }, { "title": "VEGF binding to NRP1 is essential for VEGF stimulation of endothelial cell migration, complex formation between NRP1 and VEGFR2, and signaling via FAK Tyr407 phosphorylation.", "journal": "Molecular biology of the cell", "date": "2011", "authors": "Herzog B, Pellet-Many C, Britton G, Hartzoulakis B, Zachary IC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21653826", "url": "https://glygen.org/publication/PubMed/21653826" } ] }, { "title": "Inhibiting the interaction of cMET and IGF-1R with FAK effectively reduces growth of pancreatic cancer cells in vitro and in vivo.", "journal": "Anti-cancer agents in medicinal chemistry", "date": "2013", "authors": "Ucar DA, Magis AT, He DH, Lawrence NJ, Sebti SM, Kurenova E, Zajac-Kaye M, Zhang J, Hochwald SN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23272972", "url": "https://glygen.org/publication/PubMed/23272972" } ] }, { "title": "Curcumin Suppresses Metastasis via Sp-1, FAK Inhibition, and E-Cadherin Upregulation in Colorectal Cancer.", "journal": "Evidence-based complementary and alternative medicine : eCAM", "date": "2013", "authors": "Chen CC, Sureshbabul M, Chen HW, Lin YS, Lee JY, Hong QS, Yang YC, Yu SL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" } ] }, { "title": "Focal adhesion kinase is a regulator of F-actin dynamics: New insights from studies in the testis.", "journal": "Spermatogenesis", "date": "2013", "authors": "Li SY, Mruk DD, Cheng CY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24381802", "url": "https://glygen.org/publication/PubMed/24381802" } ] }, { "title": "Therapeutic effects of tyroservatide on metastasis of lung cancer and its mechanism affecting integrin-focal adhesion kinase signal transduction.", "journal": "Drug design, development and therapy", "date": "2016", "authors": "Huang YT, Zhao L, Fu Z, Zhao M, Song XM, Jia J, Wang S, Li JP, Zhu ZF, Lin G, Lu R, Yao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" } ] }, { "title": "Raftlin is recruited by neuropilin-1 to the activated VEGFR2 complex to control proangiogenic signaling.", "journal": "Angiogenesis", "date": "2020", "authors": "Bayliss AL, Sundararaman A, Granet C, Mellor H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611" } ] }, { "title": "Molecular Basis of LH Action on Breast Cancer Cell Migration and Invasion via Kinase and Scaffold Proteins.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Mondaca Joselina Magali, Uzair Ivonne Denise, Castro Guijarro Ana Carla, Flamini Marina In\u00e9s, Sanchez Angel Matias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12871985", "url": "https://glygen.org/publication/PubMed/12871985", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15247219", "url": "https://glygen.org/publication/PubMed/15247219", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16415178", "url": "https://glygen.org/publication/PubMed/16415178", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20407018", "url": "https://glygen.org/publication/PubMed/20407018", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21653826", "url": "https://glygen.org/publication/PubMed/21653826", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23272972", "url": "https://glygen.org/publication/PubMed/23272972", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24381802", "url": "https://glygen.org/publication/PubMed/24381802", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HAVSVSETDDYAEIIDEEDT", "down_seq": "TMPSTRDYEIQRERIELGRC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr407" }, { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ], "site_lbl": "Tyr407" }, { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ], "site_lbl": "Tyr407" }, { "kinase_uniprot_canonical_ac": "Q14289-1", "kinase_gene_name": "PTK2B", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434" } ], "site_lbl": "Tyr407" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" }, { "database": "PubMed", "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591" }, { "database": "PubMed", "id": "12871985", "url": "https://glygen.org/publication/PubMed/12871985" }, { "database": "PubMed", "id": "15247219", "url": "https://glygen.org/publication/PubMed/15247219" }, { "database": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" }, { "database": "PubMed", "id": "16415178", "url": "https://glygen.org/publication/PubMed/16415178" }, { "database": "PubMed", "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" }, { "database": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" }, { "database": "PubMed", "id": "20407018", "url": "https://glygen.org/publication/PubMed/20407018" }, { "database": "PubMed", "id": "21653826", "url": "https://glygen.org/publication/PubMed/21653826" }, { "database": "PubMed", "id": "23272972", "url": "https://glygen.org/publication/PubMed/23272972" }, { "database": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" }, { "database": "PubMed", "id": "24381802", "url": "https://glygen.org/publication/PubMed/24381802" }, { "database": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" }, { "database": "PubMed", "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611" }, { "database": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ], "site_lbl": "Tyr407" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q05397-1.390.390", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05397-1.397.397", "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": 5 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q05397-1.441.441", "start_pos": 441, "end_pos": 441, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RIELGRCIGEGQFGDVHQGI", "down_seq": "MSPENPALAVAIKTCKNCTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ], "site_lbl": "Tyr441" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q05397-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q05397-1.460.460", "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": "Q05397-1.474.474", "start_pos": 474, "end_pos": 474, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "LRRK2 G2019S mutation attenuates microglial motility by inhibiting focal adhesion kinase.", "journal": "Nature communications", "date": "2015", "authors": "Choi I, Kim B, Byun JW, Baik SH, Huh YH, Kim JH, Mook-Jung I, Song WK, Shin JH, Seo H, Suh YH, Jou I, Park SM, Kang HC, Joe EH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26365310", "url": "https://glygen.org/publication/PubMed/26365310" } ] }, { "title": "LRRK2 Inhibits FAK Activity by Promoting FERM-mediated Autoinhibition of FAK and Recruiting the Tyrosine Phosphatase, SHP-2.", "journal": "Experimental neurobiology", "date": "2016", "authors": "Choi I, Byun JW, Park SM, Jou I, Joe EH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27790061", "url": "https://glygen.org/publication/PubMed/27790061" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "26365310", "url": "https://glygen.org/publication/PubMed/26365310", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27790061", "url": "https://glygen.org/publication/PubMed/27790061", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KTCKNCTSDSVREKFLQEAL", "down_seq": "MRQFDHPHIVKLIGVITENP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "26365310", "url": "https://glygen.org/publication/PubMed/26365310" }, { "database": "PubMed", "id": "27790061", "url": "https://glygen.org/publication/PubMed/27790061" } ], "site_lbl": "Thr474" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.458.458", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q05397-1.460.460", "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": "Q05397-1.503.503", "start_pos": 503, "end_pos": 503, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "IVKLIGVITENPVWIIMELC", "down_seq": "LGELRSFLQVRKYSLDLASL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ], "site_lbl": "Thr503" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q05397-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERVLKVFHYFESNSEPTTWA", "down_seq": "IIRHGDATDVRGIIQKIVDS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "site_lbl": "Ser54" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q05397-1.45.45", "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": "Q05397-1.568.568", "start_pos": 568, "end_pos": 568, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "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": "AARNVLVSSNDCVKLGDFGL", "down_seq": "RYMEDSTYYKASKGKLPIKW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser568" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q05397-1.570.570", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q05397-1.576.576", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q05397-1.577.577", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q05397-1.580.580", "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": "Q05397-1.570.570", "start_pos": 570, "end_pos": 570, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "title": "Overcoming EMT-associated resistance to anti-cancer drugs via Src/FAK pathway inhibition.", "journal": "Oncotarget", "date": "2014", "authors": "Wilson C, Nicholes K, Bustos D, Lin E, Song Q, Stephan JP, Kirkpatrick DS, Settleman J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RNVLVSSNDCVKLGDFGLSR", "down_seq": "MEDSTYYKASKGKLPIKWMA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" } ], "site_lbl": "Tyr570" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q05397-1.568.568", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q05397-1.576.576", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q05397-1.577.577", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.580.580", "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": "Q05397-1.576.576", "start_pos": 576, "end_pos": 576, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Effects of HER2 overexpression on cell signaling networks governing proliferation and migration.", "journal": "Molecular systems biology", "date": "2006", "authors": "Wolf-Yadlin A, Kumar N, Zhang Y, Hautaniemi S, Zaman M, Kim HD, Grantcharova V, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" } ] }, { "title": "Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" } ] }, { "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": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "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": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Tyrosine phosphorylation of focal adhesion kinase at sites in the catalytic domain regulates kinase activity: a role for Src family kinases.", "journal": "Molecular and cellular biology", "date": "1995", "authors": "Calalb MB, Polte TR, Hanks SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ] }, { "title": "p125Fak focal adhesion kinase is a substrate for the insulin and insulin-like growth factor-I tyrosine kinase receptors.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Baron V, Calleja V, Ferrari P, Alengrin F, Van Obberghen E", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" } ] }, { "title": "Activation of the lutropin/choriogonadotropin receptor in MA-10 cells leads to the tyrosine phosphorylation of the focal adhesion kinase by a pathway that involves Src family kinases.", "journal": "Molecular endocrinology (Baltimore, Md.)", "date": "2006", "authors": "Mizutani T, Shiraishi K, Welsh T, Ascoli M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16293639", "url": "https://glygen.org/publication/PubMed/16293639" } ] }, { "title": "Direct phosphorylation of proliferative and survival pathway proteins by RET.", "journal": "Surgery", "date": "2005", "authors": "Panta GR, Du L, Nwariaku FE, Kim LT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" } ] }, { "title": "Focal adhesion kinase (FAK) binds RET kinase via its FERM domain, priming a direct and reciprocal RET-FAK transactivation mechanism.", "journal": "The Journal of biological chemistry", "date": "2011", "authors": "Plaza-Menacho I, Morandi A, Mologni L, Boender P, Gambacorti-Passerini C, Magee AI, Hofstra RM, Knowles P, McDonald NQ, Isacke CM", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" } ] }, { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] }, { "title": "Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein.", "journal": "The Biochemical journal", "date": "2003", "authors": "Relou IA, Bax LA, van Rijn HJ, Akkerman JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ] }, { "title": "Identification of Src-specific phosphorylation site on focal adhesion kinase: dissection of the role of Src SH2 and catalytic functions and their consequences for tumor cell behavior.", "journal": "Cancer research", "date": "2005", "authors": "Brunton VG, Avizienyte E, Fincham VJ, Serrels B, Metcalf CA 3rd, Sawyer TK, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ] }, { "title": "Growth factors stimulate kidney proximal tubule cell migration independent of augmented tyrosine phosphorylation of focal adhesion kinase.", "journal": "Biochemical and biophysical research communications", "date": "2005", "authors": "Cao Y, Baig MR, Hamm LL, Wu K, Simon EE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ] }, { "title": "Phosphospecific antibodies reveal focal adhesion kinase activation loop phosphorylation in nascent and mature focal adhesions and requirement for the autophosphorylation site.", "journal": "Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research", "date": "2000-01", "authors": "Ruest P J, Roy S, Shi E, Mernaugh R L, Hanks S K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902" } ] }, { "title": "Targeting Pyk2 to beta 1-integrin-containing focal contacts rescues fibronectin-stimulated signaling and haptotactic motility defects of focal adhesion kinase-null cells.", "journal": "The Journal of cell biology", "date": "2001", "authors": "Klingbeil CK, Hauck CR, Hsia DA, Jones KC, Reider SR, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924" } ] }, { "title": "S1P induces FA remodeling in human pulmonary endothelial cells: role of Rac, GIT1, FAK, and paxillin.", "journal": "Journal of applied physiology (Bethesda, Md. : 1985)", "date": "2003", "authors": "Shikata Y, Birukov KG, Garcia JG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12482769", "url": "https://glygen.org/publication/PubMed/12482769" } ] }, { "title": "Absence of adhesion triggers differential FAK and SAPKp38 signals in SW620 human colon cancer cells that may inhibit adhesiveness and lead to cell death.", "journal": "Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology", "date": "2003", "authors": "Walsh MF, Thamilselvan V, Grotelueschen R, Farhana L, Basson M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12876384", "url": "https://glygen.org/publication/PubMed/12876384" } ] }, { "title": "Involvement of site-specific FAK phosphorylation in sphingosine-1 phosphate- and thrombin-induced focal adhesion remodeling: role of Src and GIT.", "journal": "FASEB journal : official publication of the Federation of American Societies for Experimental Biology", "date": "2003", "authors": "Shikata Y, Birukov KG, Birukova AA, Verin A, Garcia JG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14656986", "url": "https://glygen.org/publication/PubMed/14656986" } ] }, { "title": "Differential effects of shear stress and cyclic stretch on focal adhesion remodeling, site-specific FAK phosphorylation, and small GTPases in human lung endothelial cells.", "journal": "Experimental cell research", "date": "2005", "authors": "Shikata Y, Rios A, Kawkitinarong K, DePaola N, Garcia JG, Birukov KG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15707572", "url": "https://glygen.org/publication/PubMed/15707572" } ] }, { "title": "Regulation of focal adhesion dynamics and disassembly by phosphorylation of FAK at tyrosine 397.", "journal": "Journal of cell science", "date": "2005", "authors": "Hamadi A, Bouali M, Dontenwill M, Stoeckel H, Takeda K, Ronde P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16159962", "url": "https://glygen.org/publication/PubMed/16159962" } ] }, { "title": "Focal adhesion kinase promotes the aggressive melanoma phenotype.", "journal": "Cancer research", "date": "2005", "authors": "Hess AR, Postovit LM, Margaryan NV, Seftor EA, Schneider GB, Seftor RE, Nickoloff BJ, Hendrix MJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16267008", "url": "https://glygen.org/publication/PubMed/16267008" } ] }, { "title": "Elevated phosphorylation and activation of PDK-1/AKT pathway in human breast cancer.", "journal": "British journal of cancer", "date": "2005", "authors": "Lin HJ, Hsieh FC, Song H, Lin J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16288304", "url": "https://glygen.org/publication/PubMed/16288304" } ] }, { "title": "Repetitive deformation activates focal adhesion kinase and ERK mitogenic signals in human Caco-2 intestinal epithelial cells through Src and Rac1.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Chaturvedi LS, Marsh HM, Shang X, Zheng Y, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17088251", "url": "https://glygen.org/publication/PubMed/17088251" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] }, { "title": "Src and focal adhesion kinase mediate mechanical strain-induced proliferation and ERK1/2 phosphorylation in human H441 pulmonary epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2007", "authors": "Chaturvedi LS, Marsh HM, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17215324", "url": "https://glygen.org/publication/PubMed/17215324" } ] }, { "title": "EphrinA1 activates a Src/focal adhesion kinase-mediated motility response leading to rho-dependent actino/myosin contractility.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Parri M, Buricchi F, Giannoni E, Grimaldi G, Mello T, Raugei G, Ramponi G, Chiarugi P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17449913", "url": "https://glygen.org/publication/PubMed/17449913" } ] }, { "title": "Alpha-actinin-1 phosphorylation modulates pressure-induced colon cancer cell adhesion through regulation of focal adhesion kinase-Src interaction.", "journal": "American journal of physiology. Cell physiology", "date": "2007", "authors": "Craig DH, Haimovich B, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17898132", "url": "https://glygen.org/publication/PubMed/17898132" } ] }, { "title": "Multiple paxillin binding sites regulate FAK function.", "journal": "Journal of molecular signaling", "date": "2008", "authors": "Scheswohl DM, Harrell JR, Rajfur Z, Gao G, Campbell SL, Schaller MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" } ] }, { "title": "Troglitazone inhibits cell migration, adhesion, and spreading by modulating cytoskeletal rearrangement in human breast cancer cells.", "journal": "Molecular carcinogenesis", "date": "2008", "authors": "Wang PS, Chou FS, Porchia L, Saji M, Pinzone JJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18314876", "url": "https://glygen.org/publication/PubMed/18314876" } ] }, { "title": "The lysyl oxidase pro-peptide attenuates fibronectin-mediated activation of focal adhesion kinase and p130Cas in breast cancer cells.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Zhao Y, Min C, Vora SR, Trackman PC, Sonenshein GE, Kirsch KH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19029090", "url": "https://glygen.org/publication/PubMed/19029090" } ] }, { "title": "The integrin antagonist cilengitide activates alphaVbeta3, disrupts VE-cadherin localization at cell junctions and enhances permeability in endothelial cells.", "journal": "PloS one", "date": "2009", "authors": "Alghisi GC, Ponsonnet L, Ruegg C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436" } ] }, { "title": "Endothelial barrier protection by FTY720 under hyperglycemic condition: involvement of focal adhesion kinase, small GTPases, and adherens junction proteins.", "journal": "American journal of physiology. Cell physiology", "date": "2009", "authors": "Sarai K, Shikata K, Shikata Y, Omori K, Watanabe N, Sasaki M, Nishishita S, Wada J, Goda N, Kataoka N, Makino H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053" } ] }, { "title": "Focal adhesion kinase-dependent regulation of adhesive forces involves vinculin recruitment to focal adhesions.", "journal": "Biology of the cell", "date": "2010-01-14", "authors": "Dumbauld David W, Michael Kristin E, Hanks Steven K, Garc\u00eda Andr\u00e9s J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375" } ] }, { "title": "Progress in researches about focal adhesion kinase in gastrointestinal tract.", "journal": "World journal of gastroenterology", "date": "2009-12-21", "authors": "Hao Hui-Fang, Naomoto Yoshio, Bao Xiao-Hong, Watanabe Nobuyuki, Sakurama Kazufumi, Noma Kazuhiro, Tomono Yasuko, Fukazawa Takuya, Shirakawa Yasuhiro, Yamatsuji Tomoki, Matsuoka Junji, Takaoka Munenori", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455" } ] }, { "title": "JNK pathway-associated phosphatase dephosphorylates focal adhesion kinase and suppresses cell migration.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Li JP, Fu YN, Chen YR, Tan TH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849" } ] }, { "title": "The role of the focal adhesion protein PINCH1 for the radiosensitivity of adhesion and suspension cell cultures.", "journal": "PloS one", "date": "2010", "authors": "Sandfort V, Eke I, Cordes N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395" } ] }, { "title": "Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line.", "journal": "Molecular cancer", "date": "2010", "authors": "Caccia D, Micciche F, Cassinelli G, Mondellini P, Casalini P, Bongarzone I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" } ] }, { "title": "ILK mediates the effects of strain on intestinal epithelial wound closure.", "journal": "American journal of physiology. Cell physiology", "date": "2011", "authors": "Yuan L, Sanders MA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641" } ] }, { "title": "Progesterone enhances vascular endothelial cell migration via activation of focal adhesion kinase.", "journal": "Journal of cellular and molecular medicine", "date": "2012", "authors": "Zheng S, Huang J, Zhou K, Xiang Q, Zhang Y, Tan Z, Simoncini T, Fu X, Wang T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517" } ] }, { "title": "Suppression of E-cadherin function drives the early stages of Ras-induced squamous cell carcinoma through upregulation of FAK and Src.", "journal": "The Journal of investigative dermatology", "date": "2011", "authors": "Alt-Holland A, Sowalsky AG, Szwec-Levin Y, Shamis Y, Hatch H, Feig LA, Garlick JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" } ] }, { "title": "Endothelial cell-specific molecule 2 (ECSM2) localizes to cell-cell junctions and modulates bFGF-directed cell migration via the ERK-FAK pathway.", "journal": "PloS one", "date": "2011", "authors": "Shi C, Lu J, Wu W, Ma F, Georges J, Huang H, Balducci J, Chang Y, Huang Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547" } ] }, { "title": "Enhanced integrin mediated signaling and cell cycle progression on fibronectin mimetic peptide amphiphile monolayers.", "journal": "Langmuir : the ACS journal of surfaces and colloids", "date": "2012-01-24", "authors": "Shroff Kamlesh, Pearce Timothy R, Kokkoli Efrosini", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22149259", "url": "https://glygen.org/publication/PubMed/22149259" } ] }, { "title": "ADAM15 protein amplifies focal adhesion kinase phosphorylation under genotoxic stress conditions.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Fried D, Bohm BB, Krause K, Burkhardt H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741" } ] }, { "title": "Nuclear-localized focal adhesion kinase regulates inflammatory VCAM-1 expression.", "journal": "The Journal of cell biology", "date": "2012", "authors": "Lim ST, Miller NL, Chen XL, Tancioni I, Walsh CT, Lawson C, Uryu S, Weis SM, Cheresh DA, Schlaepfer DD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22734001", "url": "https://glygen.org/publication/PubMed/22734001" } ] }, { "title": "Mda-9/syntenin promotes human brain glioma migration through focal adhesion kinase (FAK)-JNK and FAK-AKT signaling.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "date": "2012", "authors": "Zhong D, Ran JH, Tang WY, Zhang XD, Tan Y, Chen GJ, Li XS, Yan Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" } ] }, { "title": "Rap1 can bypass the FAK-Src-Paxillin cascade to induce cell spreading and focal adhesion formation.", "journal": "PloS one", "date": "2012", "authors": "Ross SH, Spanjaard E, Post A, Vliem MJ, Kristyanto H, Bos JL, de Rooij J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" } ] }, { "title": "Inhibition of Src activation with cardiotoxin III blocks migration and invasion of MDA-MB-231 cells.", "journal": "Toxicon : official journal of the International Society on Toxinology", "date": "2013-11", "authors": "Tsai Pei-Chien, Chu Chiao-Lun, Chiu Chien-Chih, Chang Long-Sen, Lin Shinne-Ren", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586" } ] }, { "title": "Curcumin Suppresses Metastasis via Sp-1, FAK Inhibition, and E-Cadherin Upregulation in Colorectal Cancer.", "journal": "Evidence-based complementary and alternative medicine : eCAM", "date": "2013", "authors": "Chen CC, Sureshbabul M, Chen HW, Lin YS, Lee JY, Hong QS, Yang YC, Yu SL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" } ] }, { "title": "EGFR/MEK/ERK/CDK5-dependent integrin-independent FAK phosphorylated on serine 732 contributes to microtubule depolymerization and mitosis in tumor cells.", "journal": "Cell death & disease", "date": "2013-10-03", "authors": "Rea K, Sensi M, Anichini A, Canevari S, Tomassetti A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658" } ] }, { "title": "Naphtho[1,2-b]furan-4,5-dione inhibits MDA-MB-231 cell migration and invasion by suppressing Src-mediated signaling pathways.", "journal": "Molecular and cellular biochemistry", "date": "2014", "authors": "Tsai PC, Chu CL, Fu YS, Tseng CH, Chen YL, Chang LS, Lin SR", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24162594", "url": "https://glygen.org/publication/PubMed/24162594" } ] }, { "title": "Phosphoproteomic profiling identifies focal adhesion kinase as a mediator of docetaxel resistance in castrate-resistant prostate cancer.", "journal": "Molecular cancer therapeutics", "date": "2014", "authors": "Lee BY, Hochgrafe F, Lin HM, Castillo L, Wu J, Raftery MJ, Martin Shreeve S, Horvath LG, Daly RJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24194567", "url": "https://glygen.org/publication/PubMed/24194567" } ] }, { "title": "Low-intensity pulsed ultrasound promotes chondrogenic progenitor cell migration via focal adhesion kinase pathway.", "journal": "Ultrasound in medicine & biology", "date": "2014", "authors": "Jang KW, Ding L, Seol D, Lim TH, Buckwalter JA, Martin JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24612644", "url": "https://glygen.org/publication/PubMed/24612644" } ] }, { "title": "Altering FAK-paxillin interactions reduces adhesion, migration and invasion processes.", "journal": "PloS one", "date": "2014", "authors": "Deramaudt Th\u00e9r\u00e8se B, Dujardin Denis, Noulet Fanny, Martin Sophie, Vauchelles Romain, Takeda Ken, Rond\u00e9 Philippe", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" } ] }, { "title": "Roles of raft-anchored adaptor Cbp/PAG1 in spatial regulation of c-Src kinase.", "journal": "PloS one", "date": "2014", "authors": "Saitou T, Kajiwara K, Oneyama C, Suzuki T, Okada M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24675741", "url": "https://glygen.org/publication/PubMed/24675741" } ] }, { "title": "Biglycan enhances gastric cancer invasion by activating FAK signaling pathway.", "journal": "Oncotarget", "date": "2014", "authors": "Hu L, Duan YT, Li JF, Su LP, Yan M, Zhu ZG, Liu BY, Yang QM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" } ] }, { "title": "Wild-type and mutant p53 differentially regulate NADPH oxidase 4 in TGF-beta-mediated migration of human lung and breast epithelial cells.", "journal": "British journal of cancer", "date": "2014", "authors": "Boudreau HE, Casterline BW, Burke DJ, Leto TL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24714748", "url": "https://glygen.org/publication/PubMed/24714748" } ] }, { "title": "The marine-derived sipholenol A-4-O-3',4'-dichlorobenzoate inhibits breast cancer growth and motility in vitro and in vivo through the suppression of Brk and FAK signaling.", "journal": "Marine drugs", "date": "2014", "authors": "Akl MR, Foudah AI, Ebrahim HY, Meyer SA, El Sayed KA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" } ] }, { "title": "An aberrant spliced transcript of focal adhesion kinase is exclusively expressed in human breast cancer.", "journal": "Journal of translational medicine", "date": "2014", "authors": "Yao L, Li K, Peng W, Lin Q, Li S, Hu X, Zheng X, Shao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534" } ] }, { "title": "Maternal embryonic leucine zipper kinase enhances gastric cancer progression via the FAK/Paxillin pathway.", "journal": "Molecular cancer", "date": "2014", "authors": "Du T, Qu Y, Li J, Li H, Su L, Zhou Q, Yan M, Li C, Zhu Z, Liu B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" } ] }, { "title": "Overcoming EMT-associated resistance to anti-cancer drugs via Src/FAK pathway inhibition.", "journal": "Oncotarget", "date": "2014", "authors": "Wilson C, Nicholes K, Bustos D, Lin E, Song Q, Stephan JP, Kirkpatrick DS, Settleman J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" } ] }, { "title": "Selective inhibition of RET mediated cell proliferation in vitro by the kinase inhibitor SPP86.", "journal": "BMC cancer", "date": "2014", "authors": "Alao JP, Michlikova S, Diner P, Grotli M, Sunnerhagen P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25409876", "url": "https://glygen.org/publication/PubMed/25409876" } ] }, { "title": "Lipopolysaccharide-promoted proliferation of Caco-2 cells is mediated by c-Src induction and ERK activation.", "journal": "BioMedicine", "date": "2015", "authors": "Lin TY, Fan CW, Maa MC, Leu TH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25705585", "url": "https://glygen.org/publication/PubMed/25705585" } ] }, { "title": "N-Cadherin Induction by ECM Stiffness and FAK Overrides the Spreading Requirement for Proliferation of Vascular Smooth Muscle Cells.", "journal": "Cell reports", "date": "2015", "authors": "Mui KL, Bae YH, Gao L, Liu SL, Xu T, Radice GL, Chen CS, Assoian RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414" } ] }, { "title": "Ruthenium polypyridyl complex inhibits growth and metastasis of breast cancer cells by suppressing FAK signaling with enhancement of TRAIL-induced apoptosis.", "journal": "Scientific reports", "date": "2015", "authors": "Cao W, Zheng W, Chen T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" } ] }, { "title": "Pinocembrin suppresses TGF-\u03b21-induced epithelial-mesenchymal transition and metastasis of human Y-79 retinoblastoma cells through inactivating \u03b1v\u03b23 integrin/FAK/p38\u03b1 signaling pathway.", "journal": "Cell & bioscience", "date": "2014", "authors": "Chen Kun-Shiang, Shi Ming-Der, Chien Chi-Sheng, Shih Yuan-Wei", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790" } ] }, { "title": "The miR-130 family promotes cell migration and invasion in bladder cancer through FAK and Akt phosphorylation by regulating PTEN.", "journal": "Scientific reports", "date": "2016", "authors": "Egawa H, Jingushi K, Hirono T, Ueda Y, Kitae K, Nakata W, Fujita K, Uemura M, Nonomura N, Tsujikawa K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26837847", "url": "https://glygen.org/publication/PubMed/26837847" } ] }, { "title": "Novel Role of Src in Priming Pyk2 Phosphorylation.", "journal": "PloS one", "date": "2016", "authors": "Zhao M, Finlay D, Zharkikh I, Vuori K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" } ] }, { "title": "Therapeutic effects of tyroservatide on metastasis of lung cancer and its mechanism affecting integrin-focal adhesion kinase signal transduction.", "journal": "Drug design, development and therapy", "date": "2016", "authors": "Huang YT, Zhao L, Fu Z, Zhao M, Song XM, Jia J, Wang S, Li JP, Zhu ZF, Lin G, Lu R, Yao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" } ] }, { "title": "HER2 reduces breast cancer radiosensitivity by activating focal adhesion kinase in vitro and in vivo.", "journal": "Oncotarget", "date": "2016", "authors": "Hou J, Zhou Z, Chen X, Zhao R, Yang Z, Wei N, Ni Q, Feng Y, Yu X, Ma J, Guo X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256" } ] }, { "title": "SMARCE1 regulates metastatic potential of breast cancer cells through the HIF1A/PTK2 pathway.", "journal": "Breast cancer research : BCR", "date": "2016", "authors": "Sethuraman A, Brown M, Seagroves TN, Wu ZH, Pfeffer LM, Fan M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27495308", "url": "https://glygen.org/publication/PubMed/27495308" } ] }, { "title": "Thrombomodulin promotes focal adhesion kinase activation and contributes to angiogenesis by binding to fibronectin.", "journal": "Oncotarget", "date": "2016", "authors": "Hsu YY, Shi GY, Wang KC, Ma CY, Cheng TL, Wu HL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27602495", "url": "https://glygen.org/publication/PubMed/27602495" } ] }, { "title": "Murine Polyomavirus Cell Surface Receptors Activate Distinct Signaling Pathways Required for Infection.", "journal": "mBio", "date": "2016-11-01", "authors": "O'Hara Samantha D, Garcea Robert L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27803182", "url": "https://glygen.org/publication/PubMed/27803182" } ] }, { "title": "Kinomic profiling identifies focal adhesion kinase 1 as a therapeutic target in advanced clear cell renal cell carcinoma.", "journal": "Oncotarget", "date": "2017-04-25", "authors": "Ghosh Arindam P, Willey Christopher D, Anderson Joshua C, Welaya Karim, Chen Dongquan, Mehta Amitkumar, Ghatalia Pooja, Madan Ankit, Naik Gurudatta, Sudarshan Sunil, Sonpavde Guru", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903" } ] }, { "title": "Ponatinib promotes a G1 cell-cycle arrest of merlin/NF2-deficient human schwann cells.", "journal": "Oncotarget", "date": "2017", "authors": "Petrilli AM, Garcia J, Bott M, Klingeman Plati S, Dinh CT, Bracho OR, Yan D, Zou B, Mittal R, Telischi FF, Liu XZ, Chang LS, Welling DB, Copik AJ, Fernandez-Valle C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224" } ] }, { "title": "Calpain inhibition prevents flotillin re-ordering and Src family activation during capacitation.", "journal": "Cell and tissue research", "date": "2017", "authors": "Maldonado-Garcia D, Salgado-Lucio ML, Roa-Espitia AL, Reyes-Miguel T, Hernandez-Gonzalez EO", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28432466", "url": "https://glygen.org/publication/PubMed/28432466" } ] }, { "title": "A Short Region of Connexin43 Reduces Human Glioma Stem Cell Migration, Invasion, and Survival through Src, PTEN, and FAK.", "journal": "Stem cell reports", "date": "2017", "authors": "Jaraiz-Rodriguez M, Tabernero MD, Gonzalez-Tablas M, Otero A, Orfao A, Medina JM, Tabernero A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28712848", "url": "https://glygen.org/publication/PubMed/28712848" } ] }, { "title": "Identification of zinc finger protein of the cerebellum 5 as a survival factor of prostate and colorectal cancer cells.", "journal": "Cancer science", "date": "2017", "authors": "Satow R, Inagaki S, Kato C, Shimozawa M, Fukami K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29024195", "url": "https://glygen.org/publication/PubMed/29024195" } ] }, { "title": "The activation of SRC family kinases and focal adhesion kinase with the loss of the amplified, mutated EGFR gene contributes to the resistance to afatinib, erlotinib and osimertinib in human lung cancer cells.", "journal": "Oncotarget", "date": "2017", "authors": "Murakami Y, Sonoda K, Abe H, Watari K, Kusakabe D, Azuma K, Kawahara A, Akiba J, Oneyama C, Pachter JA, Sakai K, Nishio K, Kuwano M, Ono M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" } ] }, { "title": "Mutant FGFR3 associated with SADDAN disease causes cytoskeleton disorganization through PLCgamma1/Src-mediated paxillin hyperphosphorylation.", "journal": "The international journal of biochemistry & cell biology", "date": "2018", "authors": "Montone R, Romanelli MG, Baruzzi A, Ferrarini F, Liboi E, Lievens PM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29242050", "url": "https://glygen.org/publication/PubMed/29242050" } ] }, { "title": "Focal adhesion kinases in head and neck squamous cell carcinoma.", "journal": "Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology", "date": "2018", "authors": "Flores APC, Dias KB, Hildebrand LC, Oliveira MG, Lamers ML, Sant'Ana Filho M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29292531", "url": "https://glygen.org/publication/PubMed/29292531" } ] }, { "title": "Phosphatase of regenerating liver-3 is expressed in acute lymphoblastic leukemia and mediates leukemic cell adhesion, migration and drug resistance.", "journal": "Oncotarget", "date": "2018", "authors": "Hjort MA, Abdollahi P, Vandsemb EN, Fenstad MH, Lund B, Slordahl TS, Borset M, Ro TB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29423065", "url": "https://glygen.org/publication/PubMed/29423065" } ] }, { "title": "Impact of PKCepsilon downregulation on autophagy in glioblastoma cells.", "journal": "BMC cancer", "date": "2018", "authors": "Toton E, Romaniuk A, Konieczna N, Hofmann J, Barciszewski J, Rybczynska M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667" } ] }, { "title": "Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor.", "journal": "Oncoscience", "date": "2018", "authors": "Solanki HS, Raja R, Zhavoronkov A, Ozerov IV, Artemov AV, Advani J, Radhakrishnan A, Babu N, Puttamallesh VN, Syed N, Nanjappa V, Subbannayya T, Sahasrabuddhe NA, Patil AH, Prasad TSK, Gaykalova D, Chang X, Sathyendran R, Mathur PP, Rangarajan A, Sidransky D, Pandey A, Izumchenko E, Gowda H, Chatterjee A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29556515", "url": "https://glygen.org/publication/PubMed/29556515" } ] }, { "title": "Inhibition of epithelial cell migration and Src/FAK signaling by SIRT3.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Lee JJ, van de Ven RAH, Zaganjor E, Ng MR, Barakat A, Demmers JJPG, Finley LWS, Gonzalez Herrera KN, Hung YP, Harris IS, Jeong SM, Danuser G, McAllister SS, Haigis MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029" } ] }, { "title": "Cytotoxic activity of Shp2 inhibitor fumosorinone in human cancer cells.", "journal": "Oncology letters", "date": "2018", "authors": "Chen C, Xue T, Fan P, Meng L, Wei J, Luo D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374" } ] }, { "title": "CX3CL1/fractalkine enhances prostate cancer spinal metastasis by activating the Src/FAK pathway.", "journal": "International journal of oncology", "date": "2018", "authors": "Liu P, Liang Y, Jiang L, Wang H, Wang S, Dong J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30066854", "url": "https://glygen.org/publication/PubMed/30066854" } ] }, { "title": "Bivalent Ligand UDCA-LPE Inhibits Pro-Fibrogenic Integrin Signalling by Inducing Lipid Raft-Mediated Internalization.", "journal": "International journal of molecular sciences", "date": "2018", "authors": "Su J, Gan-Schreier H, Goeppert B, Chamulitrat W, Stremmel W, Pathil A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" } ] }, { "title": "FAM129B promoted tumor invasion and proliferation via facilitating the phosphorylation of FAK signaling and associated with adverse clinical outcome of non-small cell lung cancer patients.", "journal": "OncoTargets and therapy", "date": "2018", "authors": "Zhou X, Yang F, Zhang Q, Miao Y, Hu X, Li A, Hou G, Wang Q, Kang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362" } ] }, { "title": "Inhibition of FAK Signaling Elicits Lamin A/C-Associated Nuclear Deformity and Cellular Senescence.", "journal": "Frontiers in oncology", "date": "2019", "authors": "Chuang Hsiang-Hao, Wang Pei-Hui, Niu Sheng-Wen, Zhen Yen-Yi, Huang Ming-Shyan, Hsiao Michael, Yang Chih-Jen", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269" } ] }, { "title": "Arecoline Promotes Migration of A549 Lung Cancer Cells through Activating the EGFR/Src/FAK Pathway.", "journal": "Toxins", "date": "2019", "authors": "Chang CH, Chen MC, Chiu TH, Li YH, Yu WC, Liao WL, Oner M, Yu CR, Wu CC, Yang TY, Teng CJ, Chiu KY, Chen KC, Wang HY, Yue CH, Lai CH, Hsieh JT, Lin H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30925742", "url": "https://glygen.org/publication/PubMed/30925742" } ] }, { "title": "Focal adhesion kinase (FAK) phosphorylation is a key regulator of embryonal rhabdomyosarcoma (ERMS) cell viability and migration.", "journal": "Journal of cancer research and clinical oncology", "date": "2019", "authors": "Al-Ghabkari A, Qasrawi DO, Alshehri M, Narendran A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845" } ] }, { "title": "Oxymatrine reverses epithelial-mesenchymal transition in breast cancer cells by depressing \u03b1\u2164\u03b23 integrin/FAK/PI3K/Akt signaling activation.", "journal": "OncoTargets and therapy", "date": "2019", "authors": "Chen Yan, Chen Lin, Zhang Jing-Yu, Chen Zong-Yue, Liu Ting-Ting, Zhang Yan-Yan, Fu Ling-Yun, Fan Shuang-Qin, Zhang Min-Qin, Gan Shi-Quan, Zhang Nen-Ling, Shen Xiang-Chun", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31496729", "url": "https://glygen.org/publication/PubMed/31496729" } ] }, { "title": "Glucose Transporter 1 Promotes the Malignant Phenotype of Non-Small Cell Lung Cancer through Integrin \u03b21/Src/FAK Signaling.", "journal": "Journal of Cancer", "date": "2019", "authors": "Zhao Huanyu, Sun Jian, Shao Jianshuang, Zou Zifang, Qiu Xueshan, Wang Enhua, Wu Guangping", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31598171", "url": "https://glygen.org/publication/PubMed/31598171" } ] }, { "title": "Leptin induces cell migration and invasion in a FAK-Src-dependent manner in breast cancer cells.", "journal": "Endocrine connections", "date": "2019-11", "authors": "Ju\u00e1rez-Cruz Juan Carlos, Zu\u00f1iga-Eulogio Miriam Daniela, Olea-Flores Monserrat, Casta\u00f1eda-Saucedo Eduardo, Mendoza-Catal\u00e1n Miguel \u00c1ngel, Ortu\u00f1o-Pineda Carlos, Moreno-God\u00ednez Ma Elena, Villegas-Comonfort S\u00f3crates, Padilla-Benavides Teresita, Navarro-Tito Napole\u00f3n", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408" } ] }, { "title": "Pleckstrin homology domain of phospholipase D2 is a negative regulator of focal adhesion kinase.", "journal": "BMB reports", "date": "2021-02", "authors": "Kim Mi Kyoung, Hwang Won Chan, Min Do Sik", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" } ] }, { "title": "Exosome-derived ENO1 regulates integrin \u03b16\u03b24 expression and promotes hepatocellular carcinoma growth and metastasis.", "journal": "Cell death & disease", "date": "2020-11-12", "authors": "Jiang Keqiu, Dong Chengyong, Yin Zeli, Li Rui, Mao Jiakai, Wang Chengye, Zhang Junlin, Gao Zhenming, Liang Rui, Wang Qi, Wang Liming", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263" } ] }, { "title": "FAK displacement from focal adhesions: a promising strategy to target processes implicated in cancer progression and metastasis.", "journal": "Cell communication and signaling : CCS", "date": "2021-01-07", "authors": "Antoniades Ioanna, Kyriakou Maria, Charalambous Anna, Kalalidou Katerina, Christodoulou Andri, Christoforou Maria, Skourides Paris A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438" } ] }, { "title": "Molecular Basis of LH Action on Breast Cancer Cell Migration and Invasion via Kinase and Scaffold Proteins.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Mondaca Joselina Magali, Uzair Ivonne Denise, Castro Guijarro Ana Carla, Flamini Marina In\u00e9s, Sanchez Angel Matias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" } ] }, { "title": "hTERT Downregulation Attenuates Resistance to DOX, Impairs FAK-Mediated Adhesion, and Leads to Autophagy Induction in Breast Cancer Cells.", "journal": "Cells", "date": "2021-04-10", "authors": "Romaniuk-Drapa\u0142a Aleksandra, Toto\u0144 Ewa, Konieczna Natalia, Machnik Marta, Barczak Wojciech, Kowal Dagmar, Kopczy\u0144ski Przemys\u0142aw, Kaczmarek Mariusz, Rubi\u015b B\u0142a\u017cej", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284" } ] }, { "title": "Opposite Effects of Src Family Kinases on YAP and ERK Activation in Pancreatic Cancer Cells: Implications for Targeted Therapy.", "journal": "Molecular cancer therapeutics", "date": "2022-11-03", "authors": "Sinnett-Smith James, Anwar Tarique, Reed Elaine F, Teper Yaroslav, Eibl Guido, Rozengurt Enrique", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654" } ] }, { "title": "Specific tyrosine phosphorylation of focal adhesion kinase mediated by Fer tyrosine kinase in suspended hepatocytes.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Oh MA, Choi S, Lee MJ, Choi MC, Lee SA, Ko W, Cance WG, Oh ES, Buday L, Kim SH, Lee JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ] }, { "title": "The proto-oncogene Fgr regulates cell migration and this requires its plasma membrane localization.", "journal": "Experimental cell research", "date": "2005", "authors": "Continolo S, Baruzzi A, Majeed M, Caveggion E, Fumagalli L, Lowell CA, Berton G", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395", "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" ] }, { "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16293639", "url": "https://glygen.org/publication/PubMed/16293639", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12482769", "url": "https://glygen.org/publication/PubMed/12482769", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12876384", "url": "https://glygen.org/publication/PubMed/12876384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14656986", "url": "https://glygen.org/publication/PubMed/14656986", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15707572", "url": "https://glygen.org/publication/PubMed/15707572", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16159962", "url": "https://glygen.org/publication/PubMed/16159962", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16267008", "url": "https://glygen.org/publication/PubMed/16267008", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16288304", "url": "https://glygen.org/publication/PubMed/16288304", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17088251", "url": "https://glygen.org/publication/PubMed/17088251", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17215324", "url": "https://glygen.org/publication/PubMed/17215324", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17449913", "url": "https://glygen.org/publication/PubMed/17449913", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17898132", "url": "https://glygen.org/publication/PubMed/17898132", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18314876", "url": "https://glygen.org/publication/PubMed/18314876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19029090", "url": "https://glygen.org/publication/PubMed/19029090", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22149259", "url": "https://glygen.org/publication/PubMed/22149259", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22734001", "url": "https://glygen.org/publication/PubMed/22734001", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24162594", "url": "https://glygen.org/publication/PubMed/24162594", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24194567", "url": "https://glygen.org/publication/PubMed/24194567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24612644", "url": "https://glygen.org/publication/PubMed/24612644", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24675741", "url": "https://glygen.org/publication/PubMed/24675741", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24714748", "url": "https://glygen.org/publication/PubMed/24714748", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25409876", "url": "https://glygen.org/publication/PubMed/25409876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25705585", "url": "https://glygen.org/publication/PubMed/25705585", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26837847", "url": "https://glygen.org/publication/PubMed/26837847", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27495308", "url": "https://glygen.org/publication/PubMed/27495308", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27602495", "url": "https://glygen.org/publication/PubMed/27602495", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27803182", "url": "https://glygen.org/publication/PubMed/27803182", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28432466", "url": "https://glygen.org/publication/PubMed/28432466", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28712848", "url": "https://glygen.org/publication/PubMed/28712848", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29024195", "url": "https://glygen.org/publication/PubMed/29024195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29242050", "url": "https://glygen.org/publication/PubMed/29242050", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29292531", "url": "https://glygen.org/publication/PubMed/29292531", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29423065", "url": "https://glygen.org/publication/PubMed/29423065", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29556515", "url": "https://glygen.org/publication/PubMed/29556515", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30066854", "url": "https://glygen.org/publication/PubMed/30066854", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30925742", "url": "https://glygen.org/publication/PubMed/30925742", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31496729", "url": "https://glygen.org/publication/PubMed/31496729", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31598171", "url": "https://glygen.org/publication/PubMed/31598171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SNDCVKLGDFGLSRYMEDST", "down_seq": "YKASKGKLPIKWMAPESINF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06213-1", "kinase_gene_name": "INSR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "P06241-1", "kinase_gene_name": "FYN", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16293639", "url": "https://glygen.org/publication/PubMed/16293639" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "P07947-1", "kinase_gene_name": "YES1", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16293639", "url": "https://glygen.org/publication/PubMed/16293639" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "P07949-1", "kinase_gene_name": "RET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" }, { "database": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" }, { "database": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "P09769-1", "kinase_gene_name": "FGR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17016520", "url": "https://glygen.org/publication/PubMed/17016520" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ], "site_lbl": "Tyr576" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by RET and SRC", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902" }, { "database": "PubMed", "id": "11149924", "url": "https://glygen.org/publication/PubMed/11149924" }, { "database": "PubMed", "id": "12482769", "url": "https://glygen.org/publication/PubMed/12482769" }, { "database": "PubMed", "id": "12876384", "url": "https://glygen.org/publication/PubMed/12876384" }, { "database": "PubMed", "id": "14656986", "url": "https://glygen.org/publication/PubMed/14656986" }, { "database": "PubMed", "id": "15707572", "url": "https://glygen.org/publication/PubMed/15707572" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" }, { "database": "PubMed", "id": "16159962", "url": "https://glygen.org/publication/PubMed/16159962" }, { "database": "PubMed", "id": "16267008", "url": "https://glygen.org/publication/PubMed/16267008" }, { "database": "PubMed", "id": "16288304", "url": "https://glygen.org/publication/PubMed/16288304" }, { "database": "PubMed", "id": "17088251", "url": "https://glygen.org/publication/PubMed/17088251" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" }, { "database": "PubMed", "id": "17215324", "url": "https://glygen.org/publication/PubMed/17215324" }, { "database": "PubMed", "id": "17449913", "url": "https://glygen.org/publication/PubMed/17449913" }, { "database": "PubMed", "id": "17898132", "url": "https://glygen.org/publication/PubMed/17898132" }, { "database": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" }, { "database": "PubMed", "id": "18314876", "url": "https://glygen.org/publication/PubMed/18314876" }, { "database": "PubMed", "id": "19029090", "url": "https://glygen.org/publication/PubMed/19029090" }, { "database": "PubMed", "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436" }, { "database": "PubMed", "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053" }, { "database": "PubMed", "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375" }, { "database": "PubMed", "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455" }, { "database": "PubMed", "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849" }, { "database": "PubMed", "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395" }, { "database": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" }, { "database": "PubMed", "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641" }, { "database": "PubMed", "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517" }, { "database": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" }, { "database": "PubMed", "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547" }, { "database": "PubMed", "id": "22149259", "url": "https://glygen.org/publication/PubMed/22149259" }, { "database": "PubMed", "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741" }, { "database": "PubMed", "id": "22734001", "url": "https://glygen.org/publication/PubMed/22734001" }, { "database": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" }, { "database": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" }, { "database": "PubMed", "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586" }, { "database": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" }, { "database": "PubMed", "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658" }, { "database": "PubMed", "id": "24162594", "url": "https://glygen.org/publication/PubMed/24162594" }, { "database": "PubMed", "id": "24194567", "url": "https://glygen.org/publication/PubMed/24194567" }, { "database": "PubMed", "id": "24612644", "url": "https://glygen.org/publication/PubMed/24612644" }, { "database": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" }, { "database": "PubMed", "id": "24675741", "url": "https://glygen.org/publication/PubMed/24675741" }, { "database": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" }, { "database": "PubMed", "id": "24714748", "url": "https://glygen.org/publication/PubMed/24714748" }, { "database": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" }, { "database": "PubMed", "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534" }, { "database": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" }, { "database": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" }, { "database": "PubMed", "id": "25409876", "url": "https://glygen.org/publication/PubMed/25409876" }, { "database": "PubMed", "id": "25705585", "url": "https://glygen.org/publication/PubMed/25705585" }, { "database": "PubMed", "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414" }, { "database": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" }, { "database": "PubMed", "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790" }, { "database": "PubMed", "id": "26837847", "url": "https://glygen.org/publication/PubMed/26837847" }, { "database": "PubMed", "id": "26866924", "url": "https://glygen.org/publication/PubMed/26866924" }, { "database": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" }, { "database": "PubMed", "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256" }, { "database": "PubMed", "id": "27495308", "url": "https://glygen.org/publication/PubMed/27495308" }, { "database": "PubMed", "id": "27602495", "url": "https://glygen.org/publication/PubMed/27602495" }, { "database": "PubMed", "id": "27803182", "url": "https://glygen.org/publication/PubMed/27803182" }, { "database": "PubMed", "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903" }, { "database": "PubMed", "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224" }, { "database": "PubMed", "id": "28432466", "url": "https://glygen.org/publication/PubMed/28432466" }, { "database": "PubMed", "id": "28712848", "url": "https://glygen.org/publication/PubMed/28712848" }, { "database": "PubMed", "id": "29024195", "url": "https://glygen.org/publication/PubMed/29024195" }, { "database": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" }, { "database": "PubMed", "id": "29242050", "url": "https://glygen.org/publication/PubMed/29242050" }, { "database": "PubMed", "id": "29292531", "url": "https://glygen.org/publication/PubMed/29292531" }, { "database": "PubMed", "id": "29423065", "url": "https://glygen.org/publication/PubMed/29423065" }, { "database": "PubMed", "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667" }, { "database": "PubMed", "id": "29556515", "url": "https://glygen.org/publication/PubMed/29556515" }, { "database": "PubMed", "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029" }, { "database": "PubMed", "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374" }, { "database": "PubMed", "id": "30066854", "url": "https://glygen.org/publication/PubMed/30066854" }, { "database": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" }, { "database": "PubMed", "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362" }, { "database": "PubMed", "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269" }, { "database": "PubMed", "id": "30925742", "url": "https://glygen.org/publication/PubMed/30925742" }, { "database": "PubMed", "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845" }, { "database": "PubMed", "id": "31496729", "url": "https://glygen.org/publication/PubMed/31496729" }, { "database": "PubMed", "id": "31598171", "url": "https://glygen.org/publication/PubMed/31598171" }, { "database": "PubMed", "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408" }, { "database": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" }, { "database": "PubMed", "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263" }, { "database": "PubMed", "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438" }, { "database": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" }, { "database": "PubMed", "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284" }, { "database": "PubMed", "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" }, { "database": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" }, { "database": "PubMed", "id": "15561106", "url": "https://glygen.org/publication/PubMed/15561106" } ], "site_lbl": "Tyr576" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q05397-1.568.568", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q05397-1.570.570", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q05397-1.577.577", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q05397-1.580.580", "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": 9 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 102 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.577.577", "start_pos": 577, "end_pos": 577, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Tyrosine phosphorylation of focal adhesion kinase at sites in the catalytic domain regulates kinase activity: a role for Src family kinases.", "journal": "Molecular and cellular biology", "date": "1995", "authors": "Calalb MB, Polte TR, Hanks SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ] }, { "title": "p125Fak focal adhesion kinase is a substrate for the insulin and insulin-like growth factor-I tyrosine kinase receptors.", "journal": "The Journal of biological chemistry", "date": "1998", "authors": "Baron V, Calleja V, Ferrari P, Alengrin F, Van Obberghen E", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" } ] }, { "title": "Direct phosphorylation of proliferative and survival pathway proteins by RET.", "journal": "Surgery", "date": "2005", "authors": "Panta GR, Du L, Nwariaku FE, Kim LT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" } ] }, { "title": "Focal adhesion kinase (FAK) binds RET kinase via its FERM domain, priming a direct and reciprocal RET-FAK transactivation mechanism.", "journal": "The Journal of biological chemistry", "date": "2011", "authors": "Plaza-Menacho I, Morandi A, Mologni L, Boender P, Gambacorti-Passerini C, Magee AI, Hofstra RM, Knowles P, McDonald NQ, Isacke CM", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" } ] }, { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] }, { "title": "Identification of Src-specific phosphorylation site on focal adhesion kinase: dissection of the role of Src SH2 and catalytic functions and their consequences for tumor cell behavior.", "journal": "Cancer research", "date": "2005", "authors": "Brunton VG, Avizienyte E, Fincham VJ, Serrels B, Metcalf CA 3rd, Sawyer TK, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ] }, { "title": "Tyrosine kinase BMX phosphorylates phosphotyrosine-primed motif mediating the activation of multiple receptor tyrosine kinases.", "journal": "Science signaling", "date": "2013", "authors": "Chen S, Jiang X, Gewinner CA, Asara JM, Simon NI, Cai C, Cantley LC, Balk SP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23716717", "url": "https://glygen.org/publication/PubMed/23716717" } ] }, { "title": "Growth factors stimulate kidney proximal tubule cell migration independent of augmented tyrosine phosphorylation of focal adhesion kinase.", "journal": "Biochemical and biophysical research communications", "date": "2005", "authors": "Cao Y, Baig MR, Hamm LL, Wu K, Simon EE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ] }, { "title": "Phosphospecific antibodies reveal focal adhesion kinase activation loop phosphorylation in nascent and mature focal adhesions and requirement for the autophosphorylation site.", "journal": "Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research", "date": "2000-01", "authors": "Ruest P J, Roy S, Shi E, Mernaugh R L, Hanks S K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902" } ] }, { "title": "Differential regulation of components of the focal adhesion complex by heregulin: role of phosphatase SHP-2.", "journal": "Journal of cellular physiology", "date": "2002", "authors": "Vadlamudi RK, Adam L, Nguyen D, Santos M, Kumar R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11807823", "url": "https://glygen.org/publication/PubMed/11807823" } ] }, { "title": "Regulation of CXCR4-mediated chemotaxis and chemoinvasion of breast cancer cells.", "journal": "Oncogene", "date": "2004", "authors": "Fernandis AZ, Prasad A, Band H, Klosel R, Ganju RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14712221", "url": "https://glygen.org/publication/PubMed/14712221" } ] }, { "title": "Disruption of Ca2+-dependent cell-matrix adhesion enhances c-Src kinase activity, but causes dissociation of the c-Src/FAK complex and dephosphorylation of tyrosine-577 of FAK in carcinoma cells.", "journal": "Experimental cell research", "date": "2004-02-01", "authors": "Lin Eva H, Hui Angela Y, Meens Jalna A, Tremblay Eric A, Schaefer Erik, Elliott Bruce E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14729052", "url": "https://glygen.org/publication/PubMed/14729052" } ] }, { "title": "Role of Src-specific phosphorylation site on focal adhesion kinase for senescence-associated apoptosis resistance.", "journal": "Apoptosis : an international journal on programmed cell death", "date": "2006", "authors": "Ryu SJ, Cho KA, Oh YS, Park SC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16523241", "url": "https://glygen.org/publication/PubMed/16523241" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] }, { "title": "EphrinA1 activates a Src/focal adhesion kinase-mediated motility response leading to rho-dependent actino/myosin contractility.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Parri M, Buricchi F, Giannoni E, Grimaldi G, Mello T, Raugei G, Ramponi G, Chiarugi P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17449913", "url": "https://glygen.org/publication/PubMed/17449913" } ] }, { "title": "Multiple paxillin binding sites regulate FAK function.", "journal": "Journal of molecular signaling", "date": "2008", "authors": "Scheswohl DM, Harrell JR, Rajfur Z, Gao G, Campbell SL, Schaller MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" } ] }, { "title": "The integrin antagonist cilengitide activates alphaVbeta3, disrupts VE-cadherin localization at cell junctions and enhances permeability in endothelial cells.", "journal": "PloS one", "date": "2009", "authors": "Alghisi GC, Ponsonnet L, Ruegg C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436" } ] }, { "title": "Specific tyrosine phosphorylation of focal adhesion kinase mediated by Fer tyrosine kinase in suspended hepatocytes.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Oh MA, Choi S, Lee MJ, Choi MC, Lee SA, Ko W, Cance WG, Oh ES, Buday L, Kim SH, Lee JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ] }, { "title": "Therapeutic targeting of the focal adhesion complex prevents oncogenic TGF-beta signaling and metastasis.", "journal": "Breast cancer research : BCR", "date": "2009", "authors": "Wendt MK, Schiemann WP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433" } ] }, { "title": "Focal adhesion kinase-dependent regulation of adhesive forces involves vinculin recruitment to focal adhesions.", "journal": "Biology of the cell", "date": "2010-01-14", "authors": "Dumbauld David W, Michael Kristin E, Hanks Steven K, Garc\u00eda Andr\u00e9s J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375" } ] }, { "title": "Oleic acid promotes migration on MDA-MB-231 breast cancer cells through an arachidonic acid-dependent pathway.", "journal": "The international journal of biochemistry & cell biology", "date": "2010", "authors": "Navarro-Tito N, Soto-Guzman A, Castro-Sanchez L, Martinez-Orozco R, Salazar EP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19931412", "url": "https://glygen.org/publication/PubMed/19931412" } ] }, { "title": "Progress in researches about focal adhesion kinase in gastrointestinal tract.", "journal": "World journal of gastroenterology", "date": "2009-12-21", "authors": "Hao Hui-Fang, Naomoto Yoshio, Bao Xiao-Hong, Watanabe Nobuyuki, Sakurama Kazufumi, Noma Kazuhiro, Tomono Yasuko, Fukazawa Takuya, Shirakawa Yasuhiro, Yamatsuji Tomoki, Matsuoka Junji, Takaoka Munenori", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455" } ] }, { "title": "JNK pathway-associated phosphatase dephosphorylates focal adhesion kinase and suppresses cell migration.", "journal": "The Journal of biological chemistry", "date": "2010", "authors": "Li JP, Fu YN, Chen YR, Tan TH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849" } ] }, { "title": "Hydrogen peroxide activates focal adhesion kinase and c-Src by a phosphatidylinositol 3 kinase-dependent mechanism and promotes cell migration in Caco-2 cell monolayers.", "journal": "American journal of physiology. Gastrointestinal and liver physiology", "date": "2010", "authors": "Basuroy S, Dunagan M, Sheth P, Seth A, Rao RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826" } ] }, { "title": "The role of the focal adhesion protein PINCH1 for the radiosensitivity of adhesion and suspension cell cultures.", "journal": "PloS one", "date": "2010", "authors": "Sandfort V, Eke I, Cordes N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395" } ] }, { "title": "Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line.", "journal": "Molecular cancer", "date": "2010", "authors": "Caccia D, Micciche F, Cassinelli G, Mondellini P, Casalini P, Bongarzone I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" } ] }, { "title": "Progesterone enhances vascular endothelial cell migration via activation of focal adhesion kinase.", "journal": "Journal of cellular and molecular medicine", "date": "2012", "authors": "Zheng S, Huang J, Zhou K, Xiang Q, Zhang Y, Tan Z, Simoncini T, Fu X, Wang T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517" } ] }, { "title": "Suppression of E-cadherin function drives the early stages of Ras-induced squamous cell carcinoma through upregulation of FAK and Src.", "journal": "The Journal of investigative dermatology", "date": "2011", "authors": "Alt-Holland A, Sowalsky AG, Szwec-Levin Y, Shamis Y, Hatch H, Feig LA, Garlick JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" } ] }, { "title": "Endothelial cell-specific molecule 2 (ECSM2) localizes to cell-cell junctions and modulates bFGF-directed cell migration via the ERK-FAK pathway.", "journal": "PloS one", "date": "2011", "authors": "Shi C, Lu J, Wu W, Ma F, Georges J, Huang H, Balducci J, Chang Y, Huang Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547" } ] }, { "title": "Rap1 can bypass the FAK-Src-Paxillin cascade to induce cell spreading and focal adhesion formation.", "journal": "PloS one", "date": "2012", "authors": "Ross SH, Spanjaard E, Post A, Vliem MJ, Kristyanto H, Bos JL, de Rooij J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" } ] }, { "title": "Curcumin Suppresses Metastasis via Sp-1, FAK Inhibition, and E-Cadherin Upregulation in Colorectal Cancer.", "journal": "Evidence-based complementary and alternative medicine : eCAM", "date": "2013", "authors": "Chen CC, Sureshbabul M, Chen HW, Lin YS, Lee JY, Hong QS, Yang YC, Yu SL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" } ] }, { "title": "Naphtho[1,2-b]furan-4,5-dione inhibits MDA-MB-231 cell migration and invasion by suppressing Src-mediated signaling pathways.", "journal": "Molecular and cellular biochemistry", "date": "2014", "authors": "Tsai PC, Chu CL, Fu YS, Tseng CH, Chen YL, Chang LS, Lin SR", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24162594", "url": "https://glygen.org/publication/PubMed/24162594" } ] }, { "title": "Low-intensity pulsed ultrasound promotes chondrogenic progenitor cell migration via focal adhesion kinase pathway.", "journal": "Ultrasound in medicine & biology", "date": "2014", "authors": "Jang KW, Ding L, Seol D, Lim TH, Buckwalter JA, Martin JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24612644", "url": "https://glygen.org/publication/PubMed/24612644" } ] }, { "title": "Biglycan enhances gastric cancer invasion by activating FAK signaling pathway.", "journal": "Oncotarget", "date": "2014", "authors": "Hu L, Duan YT, Li JF, Su LP, Yan M, Zhu ZG, Liu BY, Yang QM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" } ] }, { "title": "The marine-derived sipholenol A-4-O-3',4'-dichlorobenzoate inhibits breast cancer growth and motility in vitro and in vivo through the suppression of Brk and FAK signaling.", "journal": "Marine drugs", "date": "2014", "authors": "Akl MR, Foudah AI, Ebrahim HY, Meyer SA, El Sayed KA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" } ] }, { "title": "An aberrant spliced transcript of focal adhesion kinase is exclusively expressed in human breast cancer.", "journal": "Journal of translational medicine", "date": "2014", "authors": "Yao L, Li K, Peng W, Lin Q, Li S, Hu X, Zheng X, Shao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534" } ] }, { "title": "Maternal embryonic leucine zipper kinase enhances gastric cancer progression via the FAK/Paxillin pathway.", "journal": "Molecular cancer", "date": "2014", "authors": "Du T, Qu Y, Li J, Li H, Su L, Zhou Q, Yan M, Li C, Zhu Z, Liu B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" } ] }, { "title": "Overcoming EMT-associated resistance to anti-cancer drugs via Src/FAK pathway inhibition.", "journal": "Oncotarget", "date": "2014", "authors": "Wilson C, Nicholes K, Bustos D, Lin E, Song Q, Stephan JP, Kirkpatrick DS, Settleman J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" } ] }, { "title": "Ruthenium polypyridyl complex inhibits growth and metastasis of breast cancer cells by suppressing FAK signaling with enhancement of TRAIL-induced apoptosis.", "journal": "Scientific reports", "date": "2015", "authors": "Cao W, Zheng W, Chen T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" } ] }, { "title": "Therapeutic effects of tyroservatide on metastasis of lung cancer and its mechanism affecting integrin-focal adhesion kinase signal transduction.", "journal": "Drug design, development and therapy", "date": "2016", "authors": "Huang YT, Zhao L, Fu Z, Zhao M, Song XM, Jia J, Wang S, Li JP, Zhu ZF, Lin G, Lu R, Yao Z", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" } ] }, { "title": "SMARCE1 regulates metastatic potential of breast cancer cells through the HIF1A/PTK2 pathway.", "journal": "Breast cancer research : BCR", "date": "2016", "authors": "Sethuraman A, Brown M, Seagroves TN, Wu ZH, Pfeffer LM, Fan M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27495308", "url": "https://glygen.org/publication/PubMed/27495308" } ] }, { "title": "Murine Polyomavirus Cell Surface Receptors Activate Distinct Signaling Pathways Required for Infection.", "journal": "mBio", "date": "2016-11-01", "authors": "O'Hara Samantha D, Garcea Robert L", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27803182", "url": "https://glygen.org/publication/PubMed/27803182" } ] }, { "title": "Phospholipid binding to the FAK catalytic domain impacts function.", "journal": "PloS one", "date": "2017", "authors": "Hall Jessica E, Schaller Michael D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177" } ] }, { "title": "Kinomic profiling identifies focal adhesion kinase 1 as a therapeutic target in advanced clear cell renal cell carcinoma.", "journal": "Oncotarget", "date": "2017-04-25", "authors": "Ghosh Arindam P, Willey Christopher D, Anderson Joshua C, Welaya Karim, Chen Dongquan, Mehta Amitkumar, Ghatalia Pooja, Madan Ankit, Naik Gurudatta, Sudarshan Sunil, Sonpavde Guru", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903" } ] }, { "title": "Ponatinib promotes a G1 cell-cycle arrest of merlin/NF2-deficient human schwann cells.", "journal": "Oncotarget", "date": "2017", "authors": "Petrilli AM, Garcia J, Bott M, Klingeman Plati S, Dinh CT, Bracho OR, Yan D, Zou B, Mittal R, Telischi FF, Liu XZ, Chang LS, Welling DB, Copik AJ, Fernandez-Valle C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224" } ] }, { "title": "Calpain inhibition prevents flotillin re-ordering and Src family activation during capacitation.", "journal": "Cell and tissue research", "date": "2017", "authors": "Maldonado-Garcia D, Salgado-Lucio ML, Roa-Espitia AL, Reyes-Miguel T, Hernandez-Gonzalez EO", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28432466", "url": "https://glygen.org/publication/PubMed/28432466" } ] }, { "title": "A Short Region of Connexin43 Reduces Human Glioma Stem Cell Migration, Invasion, and Survival through Src, PTEN, and FAK.", "journal": "Stem cell reports", "date": "2017", "authors": "Jaraiz-Rodriguez M, Tabernero MD, Gonzalez-Tablas M, Otero A, Orfao A, Medina JM, Tabernero A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28712848", "url": "https://glygen.org/publication/PubMed/28712848" } ] }, { "title": "Identification of zinc finger protein of the cerebellum 5 as a survival factor of prostate and colorectal cancer cells.", "journal": "Cancer science", "date": "2017", "authors": "Satow R, Inagaki S, Kato C, Shimozawa M, Fukami K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29024195", "url": "https://glygen.org/publication/PubMed/29024195" } ] }, { "title": "The activation of SRC family kinases and focal adhesion kinase with the loss of the amplified, mutated EGFR gene contributes to the resistance to afatinib, erlotinib and osimertinib in human lung cancer cells.", "journal": "Oncotarget", "date": "2017", "authors": "Murakami Y, Sonoda K, Abe H, Watari K, Kusakabe D, Azuma K, Kawahara A, Akiba J, Oneyama C, Pachter JA, Sakai K, Nishio K, Kuwano M, Ono M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" } ] }, { "title": "Mutant FGFR3 associated with SADDAN disease causes cytoskeleton disorganization through PLCgamma1/Src-mediated paxillin hyperphosphorylation.", "journal": "The international journal of biochemistry & cell biology", "date": "2018", "authors": "Montone R, Romanelli MG, Baruzzi A, Ferrarini F, Liboi E, Lievens PM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29242050", "url": "https://glygen.org/publication/PubMed/29242050" } ] }, { "title": "Phosphatase of regenerating liver-3 is expressed in acute lymphoblastic leukemia and mediates leukemic cell adhesion, migration and drug resistance.", "journal": "Oncotarget", "date": "2018", "authors": "Hjort MA, Abdollahi P, Vandsemb EN, Fenstad MH, Lund B, Slordahl TS, Borset M, Ro TB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29423065", "url": "https://glygen.org/publication/PubMed/29423065" } ] }, { "title": "Impact of PKCepsilon downregulation on autophagy in glioblastoma cells.", "journal": "BMC cancer", "date": "2018", "authors": "Toton E, Romaniuk A, Konieczna N, Hofmann J, Barciszewski J, Rybczynska M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667" } ] }, { "title": "Targeting focal adhesion kinase overcomes erlotinib resistance in smoke induced lung cancer by altering phosphorylation of epidermal growth factor receptor.", "journal": "Oncoscience", "date": "2018", "authors": "Solanki HS, Raja R, Zhavoronkov A, Ozerov IV, Artemov AV, Advani J, Radhakrishnan A, Babu N, Puttamallesh VN, Syed N, Nanjappa V, Subbannayya T, Sahasrabuddhe NA, Patil AH, Prasad TSK, Gaykalova D, Chang X, Sathyendran R, Mathur PP, Rangarajan A, Sidransky D, Pandey A, Izumchenko E, Gowda H, Chatterjee A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29556515", "url": "https://glygen.org/publication/PubMed/29556515" } ] }, { "title": "Inhibition of epithelial cell migration and Src/FAK signaling by SIRT3.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2018", "authors": "Lee JJ, van de Ven RAH, Zaganjor E, Ng MR, Barakat A, Demmers JJPG, Finley LWS, Gonzalez Herrera KN, Hung YP, Harris IS, Jeong SM, Danuser G, McAllister SS, Haigis MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029" } ] }, { "title": "CX3CL1/fractalkine enhances prostate cancer spinal metastasis by activating the Src/FAK pathway.", "journal": "International journal of oncology", "date": "2018", "authors": "Liu P, Liang Y, Jiang L, Wang H, Wang S, Dong J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30066854", "url": "https://glygen.org/publication/PubMed/30066854" } ] }, { "title": "Bivalent Ligand UDCA-LPE Inhibits Pro-Fibrogenic Integrin Signalling by Inducing Lipid Raft-Mediated Internalization.", "journal": "International journal of molecular sciences", "date": "2018", "authors": "Su J, Gan-Schreier H, Goeppert B, Chamulitrat W, Stremmel W, Pathil A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" } ] }, { "title": "Inhibition of FAK Signaling Elicits Lamin A/C-Associated Nuclear Deformity and Cellular Senescence.", "journal": "Frontiers in oncology", "date": "2019", "authors": "Chuang Hsiang-Hao, Wang Pei-Hui, Niu Sheng-Wen, Zhen Yen-Yi, Huang Ming-Shyan, Hsiao Michael, Yang Chih-Jen", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269" } ] }, { "title": "Focal adhesion kinase (FAK) phosphorylation is a key regulator of embryonal rhabdomyosarcoma (ERMS) cell viability and migration.", "journal": "Journal of cancer research and clinical oncology", "date": "2019", "authors": "Al-Ghabkari A, Qasrawi DO, Alshehri M, Narendran A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845" } ] }, { "title": "Glucose Transporter 1 Promotes the Malignant Phenotype of Non-Small Cell Lung Cancer through Integrin \u03b21/Src/FAK Signaling.", "journal": "Journal of Cancer", "date": "2019", "authors": "Zhao Huanyu, Sun Jian, Shao Jianshuang, Zou Zifang, Qiu Xueshan, Wang Enhua, Wu Guangping", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31598171", "url": "https://glygen.org/publication/PubMed/31598171" } ] }, { "title": "Leptin induces cell migration and invasion in a FAK-Src-dependent manner in breast cancer cells.", "journal": "Endocrine connections", "date": "2019-11", "authors": "Ju\u00e1rez-Cruz Juan Carlos, Zu\u00f1iga-Eulogio Miriam Daniela, Olea-Flores Monserrat, Casta\u00f1eda-Saucedo Eduardo, Mendoza-Catal\u00e1n Miguel \u00c1ngel, Ortu\u00f1o-Pineda Carlos, Moreno-God\u00ednez Ma Elena, Villegas-Comonfort S\u00f3crates, Padilla-Benavides Teresita, Navarro-Tito Napole\u00f3n", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408" } ] }, { "title": "Pleckstrin homology domain of phospholipase D2 is a negative regulator of focal adhesion kinase.", "journal": "BMB reports", "date": "2021-02", "authors": "Kim Mi Kyoung, Hwang Won Chan, Min Do Sik", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" } ] }, { "title": "Exosome-derived ENO1 regulates integrin \u03b16\u03b24 expression and promotes hepatocellular carcinoma growth and metastasis.", "journal": "Cell death & disease", "date": "2020-11-12", "authors": "Jiang Keqiu, Dong Chengyong, Yin Zeli, Li Rui, Mao Jiakai, Wang Chengye, Zhang Junlin, Gao Zhenming, Liang Rui, Wang Qi, Wang Liming", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263" } ] }, { "title": "FAK displacement from focal adhesions: a promising strategy to target processes implicated in cancer progression and metastasis.", "journal": "Cell communication and signaling : CCS", "date": "2021-01-07", "authors": "Antoniades Ioanna, Kyriakou Maria, Charalambous Anna, Kalalidou Katerina, Christodoulou Andri, Christoforou Maria, Skourides Paris A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438" } ] }, { "title": "Molecular Basis of LH Action on Breast Cancer Cell Migration and Invasion via Kinase and Scaffold Proteins.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Mondaca Joselina Magali, Uzair Ivonne Denise, Castro Guijarro Ana Carla, Flamini Marina In\u00e9s, Sanchez Angel Matias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" } ] }, { "title": "hTERT Downregulation Attenuates Resistance to DOX, Impairs FAK-Mediated Adhesion, and Leads to Autophagy Induction in Breast Cancer Cells.", "journal": "Cells", "date": "2021-04-10", "authors": "Romaniuk-Drapa\u0142a Aleksandra, Toto\u0144 Ewa, Konieczna Natalia, Machnik Marta, Barczak Wojciech, Kowal Dagmar, Kopczy\u0144ski Przemys\u0142aw, Kaczmarek Mariusz, Rubi\u015b B\u0142a\u017cej", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284" } ] }, { "title": "Opposite Effects of Src Family Kinases on YAP and ERK Activation in Pancreatic Cancer Cells: Implications for Targeted Therapy.", "journal": "Molecular cancer therapeutics", "date": "2022-11-03", "authors": "Sinnett-Smith James, Anwar Tarique, Reed Elaine F, Teper Yaroslav, Eibl Guido, Rozengurt Enrique", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654" } ] }, { "title": "Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein.", "journal": "The Biochemical journal", "date": "2003", "authors": "Relou IA, Bax LA, van Rijn HJ, Akkerman JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23716717", "url": "https://glygen.org/publication/PubMed/23716717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11807823", "url": "https://glygen.org/publication/PubMed/11807823", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14712221", "url": "https://glygen.org/publication/PubMed/14712221", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14729052", "url": "https://glygen.org/publication/PubMed/14729052", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16523241", "url": "https://glygen.org/publication/PubMed/16523241", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17449913", "url": "https://glygen.org/publication/PubMed/17449913", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19931412", "url": "https://glygen.org/publication/PubMed/19931412", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24162594", "url": "https://glygen.org/publication/PubMed/24162594", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24612644", "url": "https://glygen.org/publication/PubMed/24612644", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27495308", "url": "https://glygen.org/publication/PubMed/27495308", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27803182", "url": "https://glygen.org/publication/PubMed/27803182", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28432466", "url": "https://glygen.org/publication/PubMed/28432466", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28712848", "url": "https://glygen.org/publication/PubMed/28712848", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29024195", "url": "https://glygen.org/publication/PubMed/29024195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29242050", "url": "https://glygen.org/publication/PubMed/29242050", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29423065", "url": "https://glygen.org/publication/PubMed/29423065", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29556515", "url": "https://glygen.org/publication/PubMed/29556515", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30066854", "url": "https://glygen.org/publication/PubMed/30066854", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31598171", "url": "https://glygen.org/publication/PubMed/31598171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NDCVKLGDFGLSRYMEDSTY", "down_seq": "KASKGKLPIKWMAPESINFR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P06213-1", "kinase_gene_name": "INSR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" } ], "site_lbl": "Tyr577" }, { "kinase_uniprot_canonical_ac": "P07949-1", "kinase_gene_name": "RET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" }, { "database": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" }, { "database": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" } ], "site_lbl": "Tyr577" }, { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr577" }, { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ], "site_lbl": "Tyr577" }, { "kinase_uniprot_canonical_ac": "P51813-1", "kinase_gene_name": "BMX", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "23716717", "url": "https://glygen.org/publication/PubMed/23716717" } ], "site_lbl": "Tyr577" }, { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" } ], "site_lbl": "Tyr577" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine; by RET and SRC", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "7529876", "url": "https://glygen.org/publication/PubMed/7529876" }, { "database": "PubMed", "id": "9507031", "url": "https://glygen.org/publication/PubMed/9507031" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "PubMed", "id": "10672902", "url": "https://glygen.org/publication/PubMed/10672902" }, { "database": "PubMed", "id": "11807823", "url": "https://glygen.org/publication/PubMed/11807823" }, { "database": "PubMed", "id": "14712221", "url": "https://glygen.org/publication/PubMed/14712221" }, { "database": "PubMed", "id": "14729052", "url": "https://glygen.org/publication/PubMed/14729052" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" }, { "database": "PubMed", "id": "16523241", "url": "https://glygen.org/publication/PubMed/16523241" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" }, { "database": "PubMed", "id": "17449913", "url": "https://glygen.org/publication/PubMed/17449913" }, { "database": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" }, { "database": "PubMed", "id": "19212436", "url": "https://glygen.org/publication/PubMed/19212436" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" }, { "database": "PubMed", "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433" }, { "database": "PubMed", "id": "19883375", "url": "https://glygen.org/publication/PubMed/19883375" }, { "database": "PubMed", "id": "19931412", "url": "https://glygen.org/publication/PubMed/19931412" }, { "database": "PubMed", "id": "20014455", "url": "https://glygen.org/publication/PubMed/20014455" }, { "database": "PubMed", "id": "20018849", "url": "https://glygen.org/publication/PubMed/20018849" }, { "database": "PubMed", "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826" }, { "database": "PubMed", "id": "20927395", "url": "https://glygen.org/publication/PubMed/20927395" }, { "database": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" }, { "database": "PubMed", "id": "21418517", "url": "https://glygen.org/publication/PubMed/21418517" }, { "database": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" }, { "database": "PubMed", "id": "21720547", "url": "https://glygen.org/publication/PubMed/21720547" }, { "database": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" }, { "database": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" }, { "database": "PubMed", "id": "24162594", "url": "https://glygen.org/publication/PubMed/24162594" }, { "database": "PubMed", "id": "24612644", "url": "https://glygen.org/publication/PubMed/24612644" }, { "database": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" }, { "database": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" }, { "database": "PubMed", "id": "24885534", "url": "https://glygen.org/publication/PubMed/24885534" }, { "database": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" }, { "database": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" }, { "database": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" }, { "database": "PubMed", "id": "27041993", "url": "https://glygen.org/publication/PubMed/27041993" }, { "database": "PubMed", "id": "27495308", "url": "https://glygen.org/publication/PubMed/27495308" }, { "database": "PubMed", "id": "27803182", "url": "https://glygen.org/publication/PubMed/27803182" }, { "database": "PubMed", "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177" }, { "database": "PubMed", "id": "28418903", "url": "https://glygen.org/publication/PubMed/28418903" }, { "database": "PubMed", "id": "28427224", "url": "https://glygen.org/publication/PubMed/28427224" }, { "database": "PubMed", "id": "28432466", "url": "https://glygen.org/publication/PubMed/28432466" }, { "database": "PubMed", "id": "28712848", "url": "https://glygen.org/publication/PubMed/28712848" }, { "database": "PubMed", "id": "29024195", "url": "https://glygen.org/publication/PubMed/29024195" }, { "database": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" }, { "database": "PubMed", "id": "29242050", "url": "https://glygen.org/publication/PubMed/29242050" }, { "database": "PubMed", "id": "29423065", "url": "https://glygen.org/publication/PubMed/29423065" }, { "database": "PubMed", "id": "29439667", "url": "https://glygen.org/publication/PubMed/29439667" }, { "database": "PubMed", "id": "29556515", "url": "https://glygen.org/publication/PubMed/29556515" }, { "database": "PubMed", "id": "29915029", "url": "https://glygen.org/publication/PubMed/29915029" }, { "database": "PubMed", "id": "30066854", "url": "https://glygen.org/publication/PubMed/30066854" }, { "database": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" }, { "database": "PubMed", "id": "30761269", "url": "https://glygen.org/publication/PubMed/30761269" }, { "database": "PubMed", "id": "31006845", "url": "https://glygen.org/publication/PubMed/31006845" }, { "database": "PubMed", "id": "31598171", "url": "https://glygen.org/publication/PubMed/31598171" }, { "database": "PubMed", "id": "31671408", "url": "https://glygen.org/publication/PubMed/31671408" }, { "database": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" }, { "database": "PubMed", "id": "33184263", "url": "https://glygen.org/publication/PubMed/33184263" }, { "database": "PubMed", "id": "33413438", "url": "https://glygen.org/publication/PubMed/33413438" }, { "database": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" }, { "database": "PubMed", "id": "33920284", "url": "https://glygen.org/publication/PubMed/33920284" }, { "database": "PubMed", "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654" }, { "database": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ], "site_lbl": "Tyr577" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q05397-1.568.568", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q05397-1.570.570", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q05397-1.576.576", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q05397-1.580.580", "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": 7 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 68 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.580.580", "start_pos": 580, "end_pos": 580, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VKLGDFGLSRYMEDSTYYKA", "down_seq": "KGKLPIKWMAPESINFRRFT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "site_lbl": "Ser580" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q05397-1.568.568", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05397-1.570.570", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q05397-1.576.576", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q05397-1.577.577", "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": "Q05397-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of focal adhesion kinase on tyrosine 194 by Met leads to its activation through relief of autoinhibition.", "journal": "Oncogene", "date": "2011", "authors": "Chen TH, Chan PC, Chen CL, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MAAA", "down_seq": "LDPNLNHTPNSSTKTHLGTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P00533-1", "kinase_gene_name": "EGFR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr5" }, { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr5" }, { "kinase_uniprot_canonical_ac": "P09619-1", "kinase_gene_name": "PDGFRB", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20802513", "url": "https://glygen.org/publication/PubMed/20802513" } ], "site_lbl": "Tyr5" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "site_lbl": "Tyr5" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q05397-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q05397-1.13.13", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.15.15", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.16.16", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q05397-1.17.17", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q05397-1.24.24", "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": 4 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.695.695", "start_pos": 695, "end_pos": 695, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Akt1 promotes focal adhesion disassembly and cell motility through phosphorylation of FAK in growth factor-stimulated cells.", "journal": "Journal of cell science", "date": "2013", "authors": "Higuchi M, Kihara R, Okazaki T, Aoki I, Suetsugu S, Gotoh Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QLSTILEEEKAQQEERMRME", "down_seq": "RRQATVSWDSGGSDEAPPKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P31749-1", "kinase_gene_name": "AKT1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ], "site_lbl": "Ser695" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ], "site_lbl": "Ser695" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q05397-1.700.700", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.705.705", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.700.700", "start_pos": 700, "end_pos": 700, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Akt1 promotes focal adhesion disassembly and cell motility through phosphorylation of FAK in growth factor-stimulated cells.", "journal": "Journal of cell science", "date": "2013", "authors": "Higuchi M, Kihara R, Okazaki T, Aoki I, Suetsugu S, Gotoh Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LEEEKAQQEERMRMESRRQA", "down_seq": "VSWDSGGSDEAPPKPSRPGY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P31749-1", "kinase_gene_name": "AKT1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ], "site_lbl": "Thr700" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "23264741", "url": "https://glygen.org/publication/PubMed/23264741" } ], "site_lbl": "Thr700" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q05397-1.695.695", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q05397-1.705.705", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.716.716", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.705.705", "start_pos": 705, "end_pos": 705, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "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": "AQQEERMRMESRRQATVSWD", "down_seq": "GGSDEAPPKPSRPGYPSPRS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser705" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q05397-1.695.695", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q05397-1.700.700", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.716.716", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q05397-1.722.722", "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": "Q05397-1.716.716", "start_pos": 716, "end_pos": 716, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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": "RRQATVSWDSGGSDEAPPKP", "down_seq": "RPGYPSPRSSEGFYPSPQHM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser716" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.700.700", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05397-1.705.705", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q05397-1.722.722", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.726.726", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.732.732", "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": "Q05397-1.722.722", "start_pos": 722, "end_pos": 722, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulation of FAK Ser-722 phosphorylation and kinase activity by GSK3 and PP1 during cell spreading and migration.", "journal": "The Biochemical journal", "date": "2005", "authors": "Bianchi M, De Lucchini S, Marin O, Turner DL, Hanks SK, Villa-Moruzzi E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092" } ] }, { "title": "Specific tyrosine phosphorylation of focal adhesion kinase mediated by Fer tyrosine kinase in suspended hepatocytes.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Oh MA, Choi S, Lee MJ, Choi MC, Lee SA, Ko W, Cance WG, Oh ES, Buday L, Kim SH, Lee JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ] }, { "title": "Serine phosphorylation of focal adhesion kinase in interphase and mitosis: a possible role in modulating binding to p130(Cas).", "journal": "Molecular biology of the cell", "date": "2001", "authors": "Ma A, Richardson A, Schaefer EM, Parsons JT", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "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": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Nuclear compartmentalization of FAK and FRNK in cardiac myocytes.", "journal": "American journal of physiology. Heart and circulatory physiology", "date": "2006", "authors": "Yi XP, Zhou J, Huber L, Qu J, Wang X, Gerdes AM, Li F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16373587", "url": "https://glygen.org/publication/PubMed/16373587" } ] }, { "title": "PTPN12 controls PTEN and the AKT signalling to FAK and HER2 in migrating ovarian cancer cells.", "journal": "Molecular and cellular biochemistry", "date": "2013", "authors": "Villa-Moruzzi E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23212450", "url": "https://glygen.org/publication/PubMed/23212450" } ] }, { "title": "Effect of Sugars on Chlamydia trachomatis Infectivity.", "journal": "Pathogens (Basel, Switzerland)", "date": "2020-04-17", "authors": "Marziali Giacomo, Marangoni Antonella, Foschi Claudio, Re Maria Carla, Calonghi Natalia", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32316668", "url": "https://glygen.org/publication/PubMed/32316668" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "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" ] }, { "id": "16373587", "url": "https://glygen.org/publication/PubMed/16373587", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23212450", "url": "https://glygen.org/publication/PubMed/23212450", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32316668", "url": "https://glygen.org/publication/PubMed/32316668", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SWDSGGSDEAPPKPSRPGYP", "down_seq": "PRSSEGFYPSPQHMVQTNHY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P49840-1", "kinase_gene_name": "GSK3A", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092" } ], "site_lbl": "Ser722" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092" }, { "database": "PubMed", "id": "16373587", "url": "https://glygen.org/publication/PubMed/16373587" }, { "database": "PubMed", "id": "23212450", "url": "https://glygen.org/publication/PubMed/23212450" }, { "database": "PubMed", "id": "32316668", "url": "https://glygen.org/publication/PubMed/32316668" } ], "site_lbl": "Ser722" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q05397-1.705.705", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q05397-1.716.716", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q05397-1.726.726", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.732.732", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q05397-1.742.742", "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": 9 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.726.726", "start_pos": 726, "end_pos": 726, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Regulation of FAK Ser-722 phosphorylation and kinase activity by GSK3 and PP1 during cell spreading and migration.", "journal": "The Biochemical journal", "date": "2005", "authors": "Bianchi M, De Lucchini S, Marin O, Turner DL, Hanks SK, Villa-Moruzzi E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGSDEAPPKPSRPGYPSPRS", "down_seq": "EGFYPSPQHMVQTNHYQVSG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15975092", "url": "https://glygen.org/publication/PubMed/15975092" } ], "site_lbl": "Ser726" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q05397-1.716.716", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q05397-1.722.722", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q05397-1.732.732", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q05397-1.742.742", "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": "Q05397-1.732.732", "start_pos": 732, "end_pos": 732, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Serine 732 phosphorylation of FAK by Cdk5 is important for microtubule organization, nuclear movement, and neuronal migration.", "journal": "Cell", "date": "2003", "authors": "Xie Z, Sanada K, Samuels BA, Shih H, Tsai LH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12941275", "url": "https://glygen.org/publication/PubMed/12941275" } ] }, { "title": "Phosphorylation of focal adhesion kinase (FAK) on Ser732 is induced by rho-dependent kinase and is essential for proline-rich tyrosine kinase-2-mediated phosphorylation of FAK on Tyr407 in response to vascular endothelial growth factor.", "journal": "Molecular biology of the cell", "date": "2006", "authors": "Le Boeuf F, Houle F, Sussman M, Huot J", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434" } ] }, { "title": "Cdk5 phosphorylation of FAK regulates centrosome-associated miocrotubules and neuronal migration.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2004", "authors": "Xie Z, Tsai LH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14712065", "url": "https://glygen.org/publication/PubMed/14712065" } ] }, { "title": "Role of focal adhesion kinase Ser-732 phosphorylation in centrosome function during mitosis.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Park AY, Shen TL, Chien S, Guan JL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19201755", "url": "https://glygen.org/publication/PubMed/19201755" } ] }, { "title": "Class 3 semaphorin mediates dendrite growth in adult newborn neurons through Cdk5/FAK pathway.", "journal": "PloS one", "date": "2013", "authors": "Ng T, Ryu JR, Sohn JH, Tan T, Song H, Ming GL, Goh EL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23762397", "url": "https://glygen.org/publication/PubMed/23762397" } ] }, { "title": "EGFR/MEK/ERK/CDK5-dependent integrin-independent FAK phosphorylated on serine 732 contributes to microtubule depolymerization and mitosis in tumor cells.", "journal": "Cell death & disease", "date": "2013-10-03", "authors": "Rea K, Sensi M, Anichini A, Canevari S, Tomassetti A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658" } ] }, { "title": "CDK5 is essential for TGF-beta1-induced epithelial-mesenchymal transition and breast cancer progression.", "journal": "Scientific reports", "date": "2013", "authors": "Liang Q, Li L, Zhang J, Lei Y, Wang L, Liu DX, Feng J, Hou P, Yao R, Zhang Y, Huang B, Lu J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24121667", "url": "https://glygen.org/publication/PubMed/24121667" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "12941275", "url": "https://glygen.org/publication/PubMed/12941275", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "14712065", "url": "https://glygen.org/publication/PubMed/14712065", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19201755", "url": "https://glygen.org/publication/PubMed/19201755", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23762397", "url": "https://glygen.org/publication/PubMed/23762397", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24121667", "url": "https://glygen.org/publication/PubMed/24121667", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PPKPSRPGYPSPRSSEGFYP", "down_seq": "PQHMVQTNHYQVSGYPGSHG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q00535-1", "kinase_gene_name": "CDK5", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "12941275", "url": "https://glygen.org/publication/PubMed/12941275" } ], "site_lbl": "Ser732" }, { "kinase_uniprot_canonical_ac": "Q13464-1", "kinase_gene_name": "ROCK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434" } ], "site_lbl": "Ser732" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by CDK5", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "12941275", "url": "https://glygen.org/publication/PubMed/12941275" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "PubMed", "id": "14712065", "url": "https://glygen.org/publication/PubMed/14712065" }, { "database": "PubMed", "id": "16760434", "url": "https://glygen.org/publication/PubMed/16760434" }, { "database": "PubMed", "id": "19201755", "url": "https://glygen.org/publication/PubMed/19201755" }, { "database": "PubMed", "id": "23762397", "url": "https://glygen.org/publication/PubMed/23762397" }, { "database": "PubMed", "id": "24091658", "url": "https://glygen.org/publication/PubMed/24091658" }, { "database": "PubMed", "id": "24121667", "url": "https://glygen.org/publication/PubMed/24121667" } ], "site_lbl": "Ser732" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.716.716", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05397-1.722.722", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q05397-1.726.726", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.742.742", "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": 7 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.742.742", "start_pos": 742, "end_pos": 742, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Preferential phosphorylation of focal adhesion kinase tyrosine 861 is critical for mediating an anti-apoptotic response to hyperosmotic stress.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Lunn JA, Jacamo R, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SPRSSEGFYPSPQHMVQTNH", "down_seq": "QVSGYPGSHGITAMAGSIYP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681" } ], "site_lbl": "Tyr742" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q05397-1.722.722", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q05397-1.726.726", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q05397-1.732.732", "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": "Q05397-1.840.840", "start_pos": 840, "end_pos": 840, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Serine phosphorylation of focal adhesion kinase in interphase and mitosis: a possible role in modulating binding to p130(Cas).", "journal": "Molecular biology of the cell", "date": "2001", "authors": "Ma A, Richardson A, Schaefer EM, Parsons JT", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEDQRWLEKEERFLKPDVRL", "down_seq": "RGSIDREDGSLQGPIGNQHI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ], "site_lbl": "Ser840" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q05397-1.824.824", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q05397-1.843.843", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q05397-1.850.850", "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": "Q05397-1.843.843", "start_pos": 843, "end_pos": 843, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "G protein-coupled receptor activation rapidly stimulates focal adhesion kinase phosphorylation at Ser-843. Mediation by Ca2+, calmodulin, and Ca2+/calmodulin-dependent kinase II.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Fan RS, Jacamo RO, Jiang X, Sinnett-Smith J, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15845548", "url": "https://glygen.org/publication/PubMed/15845548" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Serine phosphorylation of focal adhesion kinase in interphase and mitosis: a possible role in modulating binding to p130(Cas).", "journal": "Molecular biology of the cell", "date": "2001", "authors": "Ma A, Richardson A, Schaefer EM, Parsons JT", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "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": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Fibronectin enhances viability and alters cytoskeletal functions (with effects on the phosphatidylinositol 3-kinase pathway) in small cell lung cancer.", "journal": "Journal of cellular and molecular medicine", "date": "2003", "authors": "Kijima T, Maulik G, Ma PC, Madhiwala P, Schaefer E, Salgia R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054" } ] }, { "title": "FAK phosphorylation at Ser-843 inhibits Tyr-397 phosphorylation, cell spreading and migration.", "journal": "Journal of cellular physiology", "date": "2007-02", "authors": "Jacamo Rodrigo, Jiang Xiaohua, Lunn J Adrian, Rozengurt Enrique", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17096371", "url": "https://glygen.org/publication/PubMed/17096371" } ] }, { "title": "Differential FAK phosphorylation at Ser-910, Ser-843 and Tyr-397 induced by angiotensin II, LPA and EGF in intestinal epithelial cells.", "journal": "Cellular signalling", "date": "2007", "authors": "Jiang X, Sinnett-Smith J, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116" } ] }, { "title": "Abnormalities in focal adhesion complex formation, regulation, and function in human autosomal recessive polycystic kidney disease epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2010", "authors": "Israeli S, Amsler K, Zheleznova N, Wilson PD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" } ] }, { "title": "GSK3beta inhibition blocks melanoma cell/host interactions by downregulating N-cadherin expression and decreasing FAK phosphorylation.", "journal": "The Journal of investigative dermatology", "date": "2012", "authors": "John JK, Paraiso KH, Rebecca VW, Cantini LP, Abel EV, Pagano N, Meggers E, Mathew R, Krepler C, Izumi V, Fang B, Koomen JM, Messina JL, Herlyn M, Smalley KS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22810307", "url": "https://glygen.org/publication/PubMed/22810307" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15845548", "url": "https://glygen.org/publication/PubMed/15845548", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818", "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": "12927054", "url": "https://glygen.org/publication/PubMed/12927054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17096371", "url": "https://glygen.org/publication/PubMed/17096371", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22810307", "url": "https://glygen.org/publication/PubMed/22810307", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QRWLEKEERFLKPDVRLSRG", "down_seq": "IDREDGSLQGPIGNQHIYQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q9UQM7-1", "kinase_gene_name": "CAMK2A", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15845548", "url": "https://glygen.org/publication/PubMed/15845548" } ], "site_lbl": "Ser843" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" }, { "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": "12927054", "url": "https://glygen.org/publication/PubMed/12927054" }, { "database": "PubMed", "id": "17096371", "url": "https://glygen.org/publication/PubMed/17096371" }, { "database": "PubMed", "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116" }, { "database": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" }, { "database": "PubMed", "id": "22810307", "url": "https://glygen.org/publication/PubMed/22810307" } ], "site_lbl": "Ser843" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q05397-1.824.824", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q05397-1.840.840", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q05397-1.850.850", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q05397-1.861.861", "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": 10 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.850.850", "start_pos": 850, "end_pos": 850, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Proteomics analysis of protein kinases by target class-selective prefractionation and tandem mass spectrometry.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Wissing J, Jansch L, Nimtz M, Dieterich G, Hornberger R, Keri G, Wehland J, Daub H", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERFLKPDVRLSRGSIDREDG", "down_seq": "LQGPIGNQHIYQPVGKPDPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17192257", "url": "https://glygen.org/publication/PubMed/17192257" } ], "site_lbl": "Ser850" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ], "site_lbl": "Ser850" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q05397-1.840.840", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q05397-1.843.843", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.861.861", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.861.861", "start_pos": 861, "end_pos": 861, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Direct phosphorylation of proliferative and survival pathway proteins by RET.", "journal": "Surgery", "date": "2005", "authors": "Panta GR, Du L, Nwariaku FE, Kim LT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" } ] }, { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] }, { "title": "Src-mediated coupling of focal adhesion kinase to integrin alpha(v)beta5 in vascular endothelial growth factor signaling.", "journal": "The Journal of cell biology", "date": "2002", "authors": "Eliceiri BP, Puente XS, Hood JD, Stupack DG, Schlaepfer DD, Huang XZ, Sheppard D, Cheresh DA", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11927607", "url": "https://glygen.org/publication/PubMed/11927607" } ] }, { "title": "Focal adhesion kinase tyrosine-861 is a major site of phosphorylation by Src.", "journal": "Biochemical and biophysical research communications", "date": "1996", "authors": "Calalb MB, Zhang X, Polte TR, Hanks SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336" } ] }, { "title": "Identification of Src-specific phosphorylation site on focal adhesion kinase: dissection of the role of Src SH2 and catalytic functions and their consequences for tumor cell behavior.", "journal": "Cancer research", "date": "2005", "authors": "Brunton VG, Avizienyte E, Fincham VJ, Serrels B, Metcalf CA 3rd, Sawyer TK, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ] }, { "title": "Preferential phosphorylation of focal adhesion kinase tyrosine 861 is critical for mediating an anti-apoptotic response to hyperosmotic stress.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Lunn JA, Jacamo R, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681" } ] }, { "title": "Specific tyrosine phosphorylation of focal adhesion kinase mediated by Fer tyrosine kinase in suspended hepatocytes.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Oh MA, Choi S, Lee MJ, Choi MC, Lee SA, Ko W, Cance WG, Oh ES, Buday L, Kim SH, Lee JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ] }, { "title": "Growth factors stimulate kidney proximal tubule cell migration independent of augmented tyrosine phosphorylation of focal adhesion kinase.", "journal": "Biochemical and biophysical research communications", "date": "2005", "authors": "Cao Y, Baig MR, Hamm LL, Wu K, Simon EE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ] }, { "title": "Protein tyrosine kinase 6 protects cells from anoikis by directly phosphorylating focal adhesion kinase and activating AKT.", "journal": "Oncogene", "date": "2013", "authors": "Zheng Y, Gierut J, Wang Z, Miao J, Asara JM, Tyner AL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23027128", "url": "https://glygen.org/publication/PubMed/23027128" } ] }, { "title": "Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein.", "journal": "The Biochemical journal", "date": "2003", "authors": "Relou IA, Bax LA, van Rijn HJ, Akkerman JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ] }, { "title": "Therapeutic efficacy of a novel focal adhesion kinase inhibitor TAE226 in ovarian carcinoma.", "journal": "Cancer research", "date": "2007", "authors": "Halder J, Lin YG, Merritt WM, Spannuth WA, Nick AM, Honda T, Kamat AA, Han LY, Kim TJ, Lu C, Tari AM, Bornmann W, Fernandez A, Lopez-Berestein G, Sood AK", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18006843", "url": "https://glygen.org/publication/PubMed/18006843" } ] }, { "title": "Signalling of GPI-anchored CD157 via focal adhesion kinase in MCA102 fibroblasts.", "journal": "FEBS letters", "date": "2001", "authors": "Liang F, Qi RZ, Chang CF", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11602246", "url": "https://glygen.org/publication/PubMed/11602246" } ] }, { "title": "Focal adhesion kinase in netrin-1 signaling.", "journal": "Nature neuroscience", "date": "2004", "authors": "Ren XR, Ming GL, Xie Y, Hong Y, Sun DM, Zhao ZQ, Feng Z, Wang Q, Shim S, Chen ZF, Song HJ, Mei L, Xiong WC", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "15494733", "url": "https://glygen.org/publication/PubMed/15494733" } ] }, { "title": "Nuclear localization and apoptotic regulation of an amino-terminal domain focal adhesion kinase fragment in endothelial cells.", "journal": "Biochemical and biophysical research communications", "date": "2000", "authors": "Lobo M, Zachary I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591" } ] }, { "title": "Src mediates stimulation by vascular endothelial growth factor of the phosphorylation of focal adhesion kinase at tyrosine 861, and migration and anti-apoptosis in endothelial cells.", "journal": "The Biochemical journal", "date": "2001", "authors": "Abu-Ghazaleh R, Kabir J, Jia H, Lobo M, Zachary I", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11696015", "url": "https://glygen.org/publication/PubMed/11696015" } ] }, { "title": "Staurosporine induces endothelial cell apoptosis via focal adhesion kinase dephosphorylation and focal adhesion disassembly independent of focal adhesion kinase proteolysis.", "journal": "The Biochemical journal", "date": "2002", "authors": "Kabir J, Lobo M, Zachary I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12084011", "url": "https://glygen.org/publication/PubMed/12084011" } ] }, { "title": "Heregulin and HER2 signaling selectively activates c-Src phosphorylation at tyrosine 215.", "journal": "FEBS letters", "date": "2003", "authors": "Vadlamudi RK, Sahin AA, Adam L, Wang RA, Kumar R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12753909", "url": "https://glygen.org/publication/PubMed/12753909" } ] }, { "title": "Fibronectin enhances viability and alters cytoskeletal functions (with effects on the phosphatidylinositol 3-kinase pathway) in small cell lung cancer.", "journal": "Journal of cellular and molecular medicine", "date": "2003", "authors": "Kijima T, Maulik G, Ma PC, Madhiwala P, Schaefer E, Salgia R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054" } ] }, { "title": "A novel mode for integrin-mediated signaling: tethering is required for phosphorylation of FAK Y397.", "journal": "Molecular biology of the cell", "date": "2003", "authors": "Shi Q, Boettiger D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12960434", "url": "https://glygen.org/publication/PubMed/12960434" } ] }, { "title": "Regulation of vascular endothelial growth factor receptor 2-mediated phosphorylation of focal adhesion kinase by heat shock protein 90 and Src kinase activities.", "journal": "The Journal of biological chemistry", "date": "2004", "authors": "Le Boeuf F, Houle F, Huot J", "evidence": [ { "database": "Reactome", "id": "R-HSA-4420097", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-4420097" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15247219", "url": "https://glygen.org/publication/PubMed/15247219" } ] }, { "title": "Roles played by a subset of integrin signaling molecules in cadherin-based cell-cell adhesion.", "journal": "The Journal of cell biology", "date": "2004", "authors": "Yano H, Mazaki Y, Kurokawa K, Hanks SK, Matsuda M, Sabe H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" } ] }, { "title": "A role for Mer tyrosine kinase in alphavbeta5 integrin-mediated phagocytosis of apoptotic cells.", "journal": "Journal of cell science", "date": "2005", "authors": "Wu Y, Singh S, Georgescu MM, Birge RB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15673687", "url": "https://glygen.org/publication/PubMed/15673687" } ] }, { "title": "High expression of focal adhesion kinase (p125FAK) in node-negative breast cancer is related to overexpression of HER-2/neu and activated Akt kinase but does not predict outcome.", "journal": "Breast cancer research : BCR", "date": "2005", "authors": "Schmitz KJ, Grabellus F, Callies R, Otterbach F, Wohlschlaeger J, Levkau B, Kimmig R, Schmid KW, Baba HA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15743500", "url": "https://glygen.org/publication/PubMed/15743500" } ] }, { "title": "FAK signaling is critical for ErbB-2/ErbB-3 receptor cooperation for oncogenic transformation and invasion.", "journal": "The Journal of cell biology", "date": "2005-11-07", "authors": "Benlimame Naciba, He Qiang, Jie Su, Xiao Dingzhang, Xu Ying Jie, Loignon Martin, Schlaepfer David D, Alaoui-Jamali Moulay A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754" } ] }, { "title": "Integrin alpha2-mediated ERK and calpain activation play a critical role in cell adhesion and motility via focal adhesion kinase signaling: identification of a novel signaling pathway.", "journal": "The Journal of biological chemistry", "date": "2006-03-31", "authors": "Sawhney Rajinder S, Cookson Michelle M, Omar Yasin, Hauser Jennie, Brattain Michael G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16461767", "url": "https://glygen.org/publication/PubMed/16461767" } ] }, { "title": "Integrin alpha3beta1-dependent activation of FAK/Src regulates Rac1-mediated keratinocyte polarization on laminin-5.", "journal": "The Journal of investigative dermatology", "date": "2007", "authors": "Choma DP, Milano V, Pumiglia KM, DiPersio CM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] }, { "title": "A novel low-molecular weight inhibitor of focal adhesion kinase, TAE226, inhibits glioma growth.", "journal": "Molecular carcinogenesis", "date": "2007", "authors": "Shi Q, Hjelmeland AB, Keir ST, Song L, Wickman S, Jackson D, Ohmori O, Bigner DD, Friedman HS, Rich JN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439" } ] }, { "title": "Tumor necrosis factor-alpha stimulates focal adhesion kinase activity required for mitogen-activated kinase-associated interleukin 6 expression.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Schlaepfer DD, Hou S, Lim ST, Tomar A, Yu H, Lim Y, Hanson DA, Uryu SA, Molina J, Mitra SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17438336", "url": "https://glygen.org/publication/PubMed/17438336" } ] }, { "title": "Multiple paxillin binding sites regulate FAK function.", "journal": "Journal of molecular signaling", "date": "2008", "authors": "Scheswohl DM, Harrell JR, Rajfur Z, Gao G, Campbell SL, Schaller MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" } ] }, { "title": "Inhibitory role of focal adhesion kinase on anoikis in the lung cancer cell A549.", "journal": "Cell biology international", "date": "2008", "authors": "Liu G, Meng X, Jin Y, Bai J, Zhao Y, Cui X, Chen F, Fu S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694" } ] }, { "title": "Involvement of focal adhesion kinase in cellular invasion of head and neck squamous cell carcinomas via regulation of MMP-2 expression.", "journal": "British journal of cancer", "date": "2008-04-08", "authors": "Canel M, Secades P, Garz\u00f3n-Arango M, Allonca E, Suarez C, Serrels A, Frame Mc, Brunton V, Chiara M-D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846" } ] }, { "title": "Early adhesion induces interaction of FAK and Fyn in lipid domains and activates raft-dependent Akt signaling in SW480 colon cancer cells.", "journal": "Biochimica et biophysica acta", "date": "2008", "authors": "Baillat G, Siret C, Delamarre E, Luis J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444" } ] }, { "title": "beta1-integrin mediates myelin-associated glycoprotein signaling in neuronal growth cones.", "journal": "Molecular brain", "date": "2008", "authors": "Goh EL, Young JK, Kuwako K, Tessier-Lavigne M, He Z, Griffin JW, Ming GL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18922173", "url": "https://glygen.org/publication/PubMed/18922173" } ] }, { "title": "Regulation of focal adhesion turnover by ErbB signalling in invasive breast cancer cells.", "journal": "British journal of cancer", "date": "2009-02-24", "authors": "Xu Y, Benlimame N, Su J, He Q, Alaoui-Jamali M A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626" } ] }, { "title": "Characterisation of fibronectin-mediated FAK signalling pathways in lung cancer cell migration and invasion.", "journal": "British journal of cancer", "date": "2009", "authors": "Meng XN, Jin Y, Yu Y, Bai J, Liu GY, Zhu J, Zhao YZ, Wang Z, Chen F, Lee KY, Fu SB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240" } ] }, { "title": "Inhibition of focal adhesion kinase suppresses the adverse phenotype of endocrine-resistant breast cancer cells and improves endocrine response in endocrine-sensitive cells.", "journal": "Breast cancer research and treatment", "date": "2011", "authors": "Hiscox S, Barnfather P, Hayes E, Bramble P, Christensen J, Nicholson RI, Barrett-Lee P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20354780", "url": "https://glygen.org/publication/PubMed/20354780" } ] }, { "title": "Synthetic heparan sulfate oligosaccharides inhibit endothelial cell functions essential for angiogenesis.", "journal": "PloS one", "date": "2010", "authors": "Cole CL, Hansen SU, Barath M, Rushton G, Gardiner JM, Avizienyte E, Jayson GC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20657775", "url": "https://glygen.org/publication/PubMed/20657775" } ] }, { "title": "Hyperphosphorylated FAK Delocalizes from Focal Adhesions to Membrane Ruffles.", "journal": "Journal of oncology", "date": "2010", "authors": "Hamadi A, Deramaudt TB, Takeda K, Ronde P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20847951", "url": "https://glygen.org/publication/PubMed/20847951" } ] }, { "title": "Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line.", "journal": "Molecular cancer", "date": "2010", "authors": "Caccia D, Micciche F, Cassinelli G, Mondellini P, Casalini P, Bongarzone I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" } ] }, { "title": "Cyanidin-3-glucoside inhibits ethanol-induced invasion of breast cancer cells overexpressing ErbB2.", "journal": "Molecular cancer", "date": "2010", "authors": "Xu M, Bower KA, Wang S, Frank JA, Chen G, Ding M, Wang S, Shi X, Ke Z, Luo J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21034468", "url": "https://glygen.org/publication/PubMed/21034468" } ] }, { "title": "Importance of syndecan-4 and syndecan -2 in osteoblast cell adhesion and survival mediated by a tissue transglutaminase-fibronectin complex.", "journal": "Experimental cell research", "date": "2011", "authors": "Wang Z, Telci D, Griffin M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21036168", "url": "https://glygen.org/publication/PubMed/21036168" } ] }, { "title": "Ligand-independent activation of c-Met by fibronectin and \u03b1(5)\u03b2(1)-integrin regulates ovarian cancer invasion and metastasis.", "journal": "Oncogene", "date": "2011-03-31", "authors": "Mitra A K, Sawada K, Tiwari P, Mui K, Gwin K, Lengyel E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21119598", "url": "https://glygen.org/publication/PubMed/21119598" } ] }, { "title": "Nuclear and cytoplasmic LIMK1 enhances human breast cancer progression.", "journal": "Molecular cancer", "date": "2011", "authors": "McConnell BV, Koto K, Gutierrez-Hartmann A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21682918", "url": "https://glygen.org/publication/PubMed/21682918" } ] }, { "title": "The interrelationships between Src, Cav-1 and RhoGD12 in transitional cell carcinoma of the bladder.", "journal": "British journal of cancer", "date": "2012", "authors": "Qayyum T, Fyffe G, Duncan M, McArdle PA, Hilmy M, Orange C, Halbert G, Seywright M, Horgan PG, Underwood MA, Edwards J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22353809", "url": "https://glygen.org/publication/PubMed/22353809" } ] }, { "title": "Post-radiation increase in VEGF enhances glioma cell motility in vitro.", "journal": "Radiation oncology (London, England)", "date": "2012", "authors": "Kil WJ, Tofilon PJ, Camphausen K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22356893", "url": "https://glygen.org/publication/PubMed/22356893" } ] }, { "title": "ADAM15 protein amplifies focal adhesion kinase phosphorylation under genotoxic stress conditions.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Fried D, Bohm BB, Krause K, Burkhardt H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741" } ] }, { "title": "Integrin beta5 contributes to the tumorigenic potential of breast cancer cells through the Src-FAK and MEK-ERK signaling pathways.", "journal": "Oncogene", "date": "2013", "authors": "Bianchi-Smiraglia A, Paesante S, Bakin AV", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793" } ] }, { "title": "Mda-9/syntenin promotes human brain glioma migration through focal adhesion kinase (FAK)-JNK and FAK-AKT signaling.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "date": "2012", "authors": "Zhong D, Ran JH, Tang WY, Zhang XD, Tan Y, Chen GJ, Li XS, Yan Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" } ] }, { "title": "Rap1 can bypass the FAK-Src-Paxillin cascade to induce cell spreading and focal adhesion formation.", "journal": "PloS one", "date": "2012", "authors": "Ross SH, Spanjaard E, Post A, Vliem MJ, Kristyanto H, Bos JL, de Rooij J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" } ] }, { "title": "Inhibition of Src activation with cardiotoxin III blocks migration and invasion of MDA-MB-231 cells.", "journal": "Toxicon : official journal of the International Society on Toxinology", "date": "2013-11", "authors": "Tsai Pei-Chien, Chu Chiao-Lun, Chiu Chien-Chih, Chang Long-Sen, Lin Shinne-Ren", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586" } ] }, { "title": "Curcumin Suppresses Metastasis via Sp-1, FAK Inhibition, and E-Cadherin Upregulation in Colorectal Cancer.", "journal": "Evidence-based complementary and alternative medicine : eCAM", "date": "2013", "authors": "Chen CC, Sureshbabul M, Chen HW, Lin YS, Lee JY, Hong QS, Yang YC, Yu SL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" } ] }, { "title": "A photoactivatable nanopatterned substrate for analyzing collective cell migration with precisely tuned cell-extracellular matrix ligand interactions.", "journal": "PloS one", "date": "2014", "authors": "Shimizu Yoshihisa, Boehm Heike, Yamaguchi Kazuo, Spatz Joachim P, Nakanishi Jun", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24632806", "url": "https://glygen.org/publication/PubMed/24632806" } ] }, { "title": "Altering FAK-paxillin interactions reduces adhesion, migration and invasion processes.", "journal": "PloS one", "date": "2014", "authors": "Deramaudt Th\u00e9r\u00e8se B, Dujardin Denis, Noulet Fanny, Martin Sophie, Vauchelles Romain, Takeda Ken, Rond\u00e9 Philippe", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" } ] }, { "title": "The Polycomb group protein RING1B is overexpressed in ductal breast carcinoma and is required to sustain FAK steady state levels in breast cancer epithelial cells.", "journal": "Oncotarget", "date": "2014", "authors": "Bosch A, Panoutsopoulou K, Corominas JM, Gimeno R, Moreno-Bueno G, Martin-Caballero J, Morales S, Lobato T, Martinez-Romero C, Farias EF, Mayol X, Cano A, Hernandez-Munoz I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24742605", "url": "https://glygen.org/publication/PubMed/24742605" } ] }, { "title": "Carbon ion radiation inhibits glioma and endothelial cell migration induced by secreted VEGF.", "journal": "PloS one", "date": "2014", "authors": "Liu Yang, Liu Yuanyuan, Sun Chao, Gan Lu, Zhang Luwei, Mao Aihong, Du Yuting, Zhou Rong, Zhang Hong", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24893038", "url": "https://glygen.org/publication/PubMed/24893038" } ] }, { "title": "Ethoxyfagaronine, a synthetic analogue of fagaronine that inhibits vascular endothelial growth factor-1, as a new anti-angiogeneic agent.", "journal": "Investigational new drugs", "date": "2015", "authors": "Ouchani F, Jeanne A, Thevenard J, Helesbeux JJ, Wahart A, Letinois I, Duval O, Martiny L, Charpentier E, Devy J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25404487", "url": "https://glygen.org/publication/PubMed/25404487" } ] }, { "title": "N-Cadherin Induction by ECM Stiffness and FAK Overrides the Spreading Requirement for Proliferation of Vascular Smooth Muscle Cells.", "journal": "Cell reports", "date": "2015", "authors": "Mui KL, Bae YH, Gao L, Liu SL, Xu T, Radice GL, Chen CS, Assoian RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414" } ] }, { "title": "Yes-mediated phosphorylation of focal adhesion kinase at tyrosine 861 increases metastatic potential of prostate cancer cells.", "journal": "Oncotarget", "date": "2015", "authors": "Chatterji T, Varkaris AS, Parikh NU, Song JH, Cheng CJ, Schweppe RE, Alexander S, Davis JW, Troncoso P, Friedl P, Kuang J, Lin SH, Gallick GE", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25868388", "url": "https://glygen.org/publication/PubMed/25868388" } ] }, { "title": "Cross-Phosphorylation and Interaction between Src/FAK and MAPKAP5/PRAK in Early Focal Adhesions Controls Cell Motility.", "journal": "Journal of cancer biology & research", "date": "2014", "authors": "Dwyer SF, Gelman IH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26042227", "url": "https://glygen.org/publication/PubMed/26042227" } ] }, { "title": "Reelin promotes the adhesion and drug resistance of multiple myeloma cells via integrin beta1 signaling and STAT3.", "journal": "Oncotarget", "date": "2016", "authors": "Lin L, Yan F, Zhao D, Lv M, Liang X, Dai H, Qin X, Zhang Y, Hao J, Sun X, Yin Y, Huang X, Zhang J, Lu J, Ge Q", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26848618", "url": "https://glygen.org/publication/PubMed/26848618" } ] }, { "title": "FAK tyrosine 407 organized with integrin \u03b1V\u03b25 in Hs578Ts(i)8 advanced triple-negative breast cancer cells.", "journal": "International journal of oncology", "date": "2016-05", "authors": "Payan Iliet, McDonnell Susan, Torres Haydee M, Steelant Wim F A, Van Slambrouck S\u00e9verine", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26984508", "url": "https://glygen.org/publication/PubMed/26984508" } ] }, { "title": "Nuclear expression of Lyn, a Src family kinase member, is associated with poor prognosis in renal cancer patients.", "journal": "BMC cancer", "date": "2016", "authors": "Roseweir AK, Qayyum T, Lim Z, Hammond R, MacDonald AI, Fraser S, Oades GM, Aitchison M, Jones RJ, Edwards J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26984511", "url": "https://glygen.org/publication/PubMed/26984511" } ] }, { "title": "Sulfatide interacts with and activates integrin \u03b1V\u03b23 in human hepatocellular carcinoma cells.", "journal": "Oncotarget", "date": "2016-06-14", "authors": "Wang Rong, Qi Bing, Dong Yi Wei, Cai Qian Qian, Deng Nian Hui, Chen Qi, Li Chao, Jin Yu Tong, Wu Xing Zhong", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276" } ] }, { "title": "ZEB1 induces LOXL2-mediated collagen stabilization and deposition in the extracellular matrix to drive lung cancer invasion and metastasis.", "journal": "Oncogene", "date": "2017", "authors": "Peng DH, Ungewiss C, Tong P, Byers LA, Wang J, Canales JR, Villalobos PA, Uraoka N, Mino B, Behrens C, Wistuba II, Han RI, Wanna CA, Fahrenholtz M, Grande-Allen KJ, Creighton CJ, Gibbons DL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27694892", "url": "https://glygen.org/publication/PubMed/27694892" } ] }, { "title": "MICA Expression Is Regulated by Cell Adhesion and Contact in a FAK/Src-Dependent Manner.", "journal": "Frontiers in immunology", "date": "2016", "authors": "Moncayo G, Lin D, McCarthy MT, Watson AA, O'Callaghan CA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28154561", "url": "https://glygen.org/publication/PubMed/28154561" } ] }, { "title": "Phospholipid binding to the FAK catalytic domain impacts function.", "journal": "PloS one", "date": "2017", "authors": "Hall Jessica E, Schaller Michael D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177" } ] }, { "title": "FUS-CHOP Promotes Invasion in Myxoid Liposarcoma through a SRC/FAK/RHO/ROCK-Dependent Pathway.", "journal": "Neoplasia (New York, N.Y.)", "date": "2018", "authors": "Tornin J, Hermida-Prado F, Padda RS, Gonzalez MV, Alvarez-Fernandez C, Rey V, Martinez-Cruzado L, Estupinan O, Menendez ST, Fernandez-Nevado L, Astudillo A, Rodrigo JP, Lucien F, Kim Y, Leong HS, Garcia-Pedrero JM, Rodriguez R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29190494", "url": "https://glygen.org/publication/PubMed/29190494" } ] }, { "title": "The KDEL receptor signalling cascade targets focal adhesion kinase on focal adhesions and invadopodia.", "journal": "Oncotarget", "date": "2018", "authors": "Ruggiero C, Grossi M, Fragassi G, Di Campli A, Di Ilio C, Luini A, Sallese M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29535802", "url": "https://glygen.org/publication/PubMed/29535802" } ] }, { "title": "Redistribution of Adhesive Forces through Src/FAK Drives Contact Inhibition of Locomotion in Neural Crest.", "journal": "Developmental cell", "date": "2018", "authors": "Roycroft A, Szabo A, Bahm I, Daly L, Charras G, Parsons M, Mayor R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29870718", "url": "https://glygen.org/publication/PubMed/29870718" } ] }, { "title": "Suppression of lung cancer progression by isoliquiritigenin through its metabolite 2, 4, 2', 4'-Tetrahydroxychalcone.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2018", "authors": "Chen C, Shenoy AK, Padia R, Fang D, Jing Q, Yang P, Su SB, Huang S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30285892", "url": "https://glygen.org/publication/PubMed/30285892" } ] }, { "title": "Pleckstrin homology domain of phospholipase D2 is a negative regulator of focal adhesion kinase.", "journal": "BMB reports", "date": "2021-02", "authors": "Kim Mi Kyoung, Hwang Won Chan, Min Do Sik", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" } ] }, { "title": "Molecular Basis of LH Action on Breast Cancer Cell Migration and Invasion via Kinase and Scaffold Proteins.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Mondaca Joselina Magali, Uzair Ivonne Denise, Castro Guijarro Ana Carla, Flamini Marina In\u00e9s, Sanchez Angel Matias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" } ] }, { "title": "N-terminus-independent activation of c-Src via binding to a tetraspan(in) TM4SF5 in hepatocellular carcinoma is abolished by the TM4SF5 C-terminal peptide application.", "journal": "Theranostics", "date": "2021", "authors": "Song HE, Lee Y, Kim E, Cho CY, Jung O, Lee D, Lee EG, Nam SH, Kang M, Macalino SJY, Kim JE, Jung JW, Kwon SW, Choi S, Lee JW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "34335982", "url": "https://glygen.org/publication/PubMed/34335982" } ] }, { "title": "MCPIP1 regulates focal adhesion kinase and Rho GTPase-dependent migration in clear cell renal cell carcinoma.", "journal": "European journal of pharmacology", "date": "2022", "authors": "Gorka J, Marona P, Kwapisz O, Rys J, Jura J, Miekus K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35257717", "url": "https://glygen.org/publication/PubMed/35257717" } ] }, { "title": "Opposite Effects of Src Family Kinases on YAP and ERK Activation in Pancreatic Cancer Cells: Implications for Targeted Therapy.", "journal": "Molecular cancer therapeutics", "date": "2022-11-03", "authors": "Sinnett-Smith James, Anwar Tarique, Reed Elaine F, Teper Yaroslav, Eibl Guido, Rozengurt Enrique", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11927607", "url": "https://glygen.org/publication/PubMed/11927607", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23027128", "url": "https://glygen.org/publication/PubMed/23027128", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18006843", "url": "https://glygen.org/publication/PubMed/18006843", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11602246", "url": "https://glygen.org/publication/PubMed/11602246", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15494733", "url": "https://glygen.org/publication/PubMed/15494733", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11696015", "url": "https://glygen.org/publication/PubMed/11696015", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12084011", "url": "https://glygen.org/publication/PubMed/12084011", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12753909", "url": "https://glygen.org/publication/PubMed/12753909", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12960434", "url": "https://glygen.org/publication/PubMed/12960434", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15247219", "url": "https://glygen.org/publication/PubMed/15247219", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15673687", "url": "https://glygen.org/publication/PubMed/15673687", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15743500", "url": "https://glygen.org/publication/PubMed/15743500", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16461767", "url": "https://glygen.org/publication/PubMed/16461767", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17438336", "url": "https://glygen.org/publication/PubMed/17438336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18922173", "url": "https://glygen.org/publication/PubMed/18922173", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20354780", "url": "https://glygen.org/publication/PubMed/20354780", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20657775", "url": "https://glygen.org/publication/PubMed/20657775", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20847951", "url": "https://glygen.org/publication/PubMed/20847951", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21034468", "url": "https://glygen.org/publication/PubMed/21034468", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21036168", "url": "https://glygen.org/publication/PubMed/21036168", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21119598", "url": "https://glygen.org/publication/PubMed/21119598", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21682918", "url": "https://glygen.org/publication/PubMed/21682918", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22353809", "url": "https://glygen.org/publication/PubMed/22353809", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22356893", "url": "https://glygen.org/publication/PubMed/22356893", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24632806", "url": "https://glygen.org/publication/PubMed/24632806", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24742605", "url": "https://glygen.org/publication/PubMed/24742605", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24893038", "url": "https://glygen.org/publication/PubMed/24893038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25404487", "url": "https://glygen.org/publication/PubMed/25404487", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25868388", "url": "https://glygen.org/publication/PubMed/25868388", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26042227", "url": "https://glygen.org/publication/PubMed/26042227", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26848618", "url": "https://glygen.org/publication/PubMed/26848618", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26984508", "url": "https://glygen.org/publication/PubMed/26984508", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26984511", "url": "https://glygen.org/publication/PubMed/26984511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27694892", "url": "https://glygen.org/publication/PubMed/27694892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28154561", "url": "https://glygen.org/publication/PubMed/28154561", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29190494", "url": "https://glygen.org/publication/PubMed/29190494", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29535802", "url": "https://glygen.org/publication/PubMed/29535802", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29870718", "url": "https://glygen.org/publication/PubMed/29870718", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30285892", "url": "https://glygen.org/publication/PubMed/30285892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34335982", "url": "https://glygen.org/publication/PubMed/34335982", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35257717", "url": "https://glygen.org/publication/PubMed/35257717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RGSIDREDGSLQGPIGNQHI", "down_seq": "QPVGKPDPAAPPKKPPRPGA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P07949-1", "kinase_gene_name": "RET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" } ], "site_lbl": "Tyr861" }, { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr861" }, { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11927607", "url": "https://glygen.org/publication/PubMed/11927607" }, { "database": "PubMed", "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" }, { "database": "PubMed", "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681" } ], "site_lbl": "Tyr861" }, { "kinase_uniprot_canonical_ac": "P16591-1", "kinase_gene_name": "FER", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ], "site_lbl": "Tyr861" }, { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "15694384", "url": "https://glygen.org/publication/PubMed/15694384" } ], "site_lbl": "Tyr861" }, { "kinase_uniprot_canonical_ac": "Q13882-1", "kinase_gene_name": "PTK6", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "23027128", "url": "https://glygen.org/publication/PubMed/23027128" } ], "site_lbl": "Tyr861" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" }, { "database": "PubMed", "id": "18006843", "url": "https://glygen.org/publication/PubMed/18006843" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11602246", "url": "https://glygen.org/publication/PubMed/11602246" }, { "database": "PubMed", "id": "15494733", "url": "https://glygen.org/publication/PubMed/15494733" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "PubMed", "id": "11027591", "url": "https://glygen.org/publication/PubMed/11027591" }, { "database": "PubMed", "id": "11696015", "url": "https://glygen.org/publication/PubMed/11696015" }, { "database": "PubMed", "id": "12084011", "url": "https://glygen.org/publication/PubMed/12084011" }, { "database": "PubMed", "id": "12753909", "url": "https://glygen.org/publication/PubMed/12753909" }, { "database": "PubMed", "id": "12927054", "url": "https://glygen.org/publication/PubMed/12927054" }, { "database": "PubMed", "id": "12960434", "url": "https://glygen.org/publication/PubMed/12960434" }, { "database": "PubMed", "id": "15247219", "url": "https://glygen.org/publication/PubMed/15247219" }, { "database": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" }, { "database": "PubMed", "id": "15673687", "url": "https://glygen.org/publication/PubMed/15673687" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" }, { "database": "PubMed", "id": "15743500", "url": "https://glygen.org/publication/PubMed/15743500" }, { "database": "PubMed", "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754" }, { "database": "PubMed", "id": "16461767", "url": "https://glygen.org/publication/PubMed/16461767" }, { "database": "PubMed", "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" }, { "database": "PubMed", "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439" }, { "database": "PubMed", "id": "17289681", "url": "https://glygen.org/publication/PubMed/17289681" }, { "database": "PubMed", "id": "17438336", "url": "https://glygen.org/publication/PubMed/17438336" }, { "database": "PubMed", "id": "18171471", "url": "https://glygen.org/publication/PubMed/18171471" }, { "database": "PubMed", "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694" }, { "database": "PubMed", "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846" }, { "database": "PubMed", "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444" }, { "database": "PubMed", "id": "18922173", "url": "https://glygen.org/publication/PubMed/18922173" }, { "database": "PubMed", "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626" }, { "database": "PubMed", "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240" }, { "database": "PubMed", "id": "20354780", "url": "https://glygen.org/publication/PubMed/20354780" }, { "database": "PubMed", "id": "20657775", "url": "https://glygen.org/publication/PubMed/20657775" }, { "database": "PubMed", "id": "20847951", "url": "https://glygen.org/publication/PubMed/20847951" }, { "database": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" }, { "database": "PubMed", "id": "21034468", "url": "https://glygen.org/publication/PubMed/21034468" }, { "database": "PubMed", "id": "21036168", "url": "https://glygen.org/publication/PubMed/21036168" }, { "database": "PubMed", "id": "21119598", "url": "https://glygen.org/publication/PubMed/21119598" }, { "database": "PubMed", "id": "21682918", "url": "https://glygen.org/publication/PubMed/21682918" }, { "database": "PubMed", "id": "22353809", "url": "https://glygen.org/publication/PubMed/22353809" }, { "database": "PubMed", "id": "22356893", "url": "https://glygen.org/publication/PubMed/22356893" }, { "database": "PubMed", "id": "22544741", "url": "https://glygen.org/publication/PubMed/22544741" }, { "database": "PubMed", "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793" }, { "database": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" }, { "database": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" }, { "database": "PubMed", "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586" }, { "database": "PubMed", "id": "23970932", "url": "https://glygen.org/publication/PubMed/23970932" }, { "database": "PubMed", "id": "24632806", "url": "https://glygen.org/publication/PubMed/24632806" }, { "database": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" }, { "database": "PubMed", "id": "24742605", "url": "https://glygen.org/publication/PubMed/24742605" }, { "database": "PubMed", "id": "24893038", "url": "https://glygen.org/publication/PubMed/24893038" }, { "database": "PubMed", "id": "25404487", "url": "https://glygen.org/publication/PubMed/25404487" }, { "database": "PubMed", "id": "25753414", "url": "https://glygen.org/publication/PubMed/25753414" }, { "database": "PubMed", "id": "25868388", "url": "https://glygen.org/publication/PubMed/25868388" }, { "database": "PubMed", "id": "26042227", "url": "https://glygen.org/publication/PubMed/26042227" }, { "database": "PubMed", "id": "26848618", "url": "https://glygen.org/publication/PubMed/26848618" }, { "database": "PubMed", "id": "26984508", "url": "https://glygen.org/publication/PubMed/26984508" }, { "database": "PubMed", "id": "26984511", "url": "https://glygen.org/publication/PubMed/26984511" }, { "database": "PubMed", "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276" }, { "database": "PubMed", "id": "27694892", "url": "https://glygen.org/publication/PubMed/27694892" }, { "database": "PubMed", "id": "28154561", "url": "https://glygen.org/publication/PubMed/28154561" }, { "database": "PubMed", "id": "28222177", "url": "https://glygen.org/publication/PubMed/28222177" }, { "database": "PubMed", "id": "29190494", "url": "https://glygen.org/publication/PubMed/29190494" }, { "database": "PubMed", "id": "29535802", "url": "https://glygen.org/publication/PubMed/29535802" }, { "database": "PubMed", "id": "29870718", "url": "https://glygen.org/publication/PubMed/29870718" }, { "database": "PubMed", "id": "30285892", "url": "https://glygen.org/publication/PubMed/30285892" }, { "database": "PubMed", "id": "32843133", "url": "https://glygen.org/publication/PubMed/32843133" }, { "database": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" }, { "database": "PubMed", "id": "34335982", "url": "https://glygen.org/publication/PubMed/34335982" }, { "database": "PubMed", "id": "35257717", "url": "https://glygen.org/publication/PubMed/35257717" }, { "database": "PubMed", "id": "35999654", "url": "https://glygen.org/publication/PubMed/35999654" }, { "database": "PubMed", "id": "8941336", "url": "https://glygen.org/publication/PubMed/8941336" } ], "site_lbl": "Tyr861" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q05397-1.843.843", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05397-1.850.850", "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": 7 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 76 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.887.887", "start_pos": 887, "end_pos": 887, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDPAAPPKKPPRPGAPGHLG", "down_seq": "LASLSSPADSYNEGVKLQPQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "site_lbl": "Ser887" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q05397-1.892.892", "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": "Q05397-1.892.892", "start_pos": 892, "end_pos": 892, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "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": "PPKKPPRPGAPGHLGSLASL", "down_seq": "SPADSYNEGVKLQPQEISPP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser892" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q05397-1.887.887", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q05397-1.910.910", "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": "Q05397-1.910.910", "start_pos": 910, "end_pos": 910, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "P21-activated protein kinase 1 induces colorectal cancer metastasis involving ERK activation and phosphorylation of FAK at Ser-910.", "journal": "International journal of oncology", "date": "2010", "authors": "Li LH, Zheng MH, Luo Q, Ye Q, Feng B, Lu AG, Wang ML, Chen XH, Su LP, Liu BY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20811717", "url": "https://glygen.org/publication/PubMed/20811717" } ] }, { "title": "Bombesin, lysophosphatidic acid, and epidermal growth factor rapidly stimulate focal adhesion kinase phosphorylation at Ser-910: requirement for ERK activation.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Hunger-Glaser I, Salazar EP, Sinnett-Smith J, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12692126", "url": "https://glygen.org/publication/PubMed/12692126" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Large-scale proteomics analysis of the human kinome.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Oppermann FS, Gnad F, Olsen JV, Hornberger R, Greff Z, Keri G, Mann M, Daub H", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "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": "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Serine phosphorylation of focal adhesion kinase in interphase and mitosis: a possible role in modulating binding to p130(Cas).", "journal": "Molecular biology of the cell", "date": "2001", "authors": "Ma A, Richardson A, Schaefer EM, Parsons JT", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" } ] }, { "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": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" } ] }, { "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": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" } ] }, { "title": "Phosphoproteomic analysis of primary human multiple myeloma cells.", "journal": "Journal of proteomics", "date": "2010", "authors": "Ge F, Xiao CL, Yin XF, Lu CH, Zeng HL, He QY", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "20230923", "url": "https://glygen.org/publication/PubMed/20230923" } ] }, { "title": "Differential FAK phosphorylation at Ser-910, Ser-843 and Tyr-397 induced by angiotensin II, LPA and EGF in intestinal epithelial cells.", "journal": "Cellular signalling", "date": "2007", "authors": "Jiang X, Sinnett-Smith J, Rozengurt E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116" } ] }, { "title": "Targeting of FAK Ser910 by ERK5 and PP1delta in non-stimulated and phorbol ester-stimulated cells.", "journal": "The Biochemical journal", "date": "2007-11-15", "authors": "Villa-Moruzzi Emma", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17692050", "url": "https://glygen.org/publication/PubMed/17692050" } ] }, { "title": "FAK phosphorylation by ERK primes ras-induced tyrosine dephosphorylation of FAK mediated by PIN1 and PTP-PEST.", "journal": "Molecular cell", "date": "2009-07-10", "authors": "Zheng Yanhua, Xia Yan, Hawke David, Halle Maxime, Tremblay Michel L, Gao Xiang, Zhou Xiao Zhen, Aldape Kenneth, Cobb Melanie H, Xie Keping, He Jie, Lu Zhimin", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19595712", "url": "https://glygen.org/publication/PubMed/19595712" } ] }, { "title": "Abnormalities in focal adhesion complex formation, regulation, and function in human autosomal recessive polycystic kidney disease epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2010", "authors": "Israeli S, Amsler K, Zheleznova N, Wilson PD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" } ] }, { "title": "EGF-induced ERK-activation downstream of FAK requires rac1-NADPH oxidase.", "journal": "Journal of cellular physiology", "date": "2011", "authors": "Flinder LI, Timofeeva OA, Rosseland CM, Wierod L, Huitfeldt HS, Skarpen E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21660950", "url": "https://glygen.org/publication/PubMed/21660950" } ] }, { "title": "Serine-910 phosphorylation of focal adhesion kinase is critical for sarcomere reorganization in cardiomyocyte hypertrophy.", "journal": "Cardiovascular research", "date": "2011", "authors": "Chu M, Iyengar R, Koshman YE, Kim T, Russell B, Martin JL, Heroux AL, Robia SL, Samarel AM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21937583", "url": "https://glygen.org/publication/PubMed/21937583" } ] }, { "title": "Loss of anchorage primarily induces non-apoptotic cell death in a human mammary epithelial cell line under atypical focal adhesion kinase signaling.", "journal": "Cell death & disease", "date": "2015-01-22", "authors": "Ishikawa F, Ushida K, Mori K, Shibanuma M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393" } ] }, { "title": "Overexpression of regulator of G protein signaling 11 promotes cell migration and associates with advanced stages and aggressiveness of lung adenocarcinoma.", "journal": "Oncotarget", "date": "2016", "authors": "Yang SH, Li CF, Chu PY, Ko HH, Chen LT, Chen WW, Han CH, Lung JH, Shih NY", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27105500", "url": "https://glygen.org/publication/PubMed/27105500" } ] }, { "title": "Structure of focal adhesion kinase in healthy heart versus pathological cardiac hypertrophy: A modeling and simulation study.", "journal": "Journal of molecular graphics & modelling", "date": "2018", "authors": "Mohanty P, Bhatnagar S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29306139", "url": "https://glygen.org/publication/PubMed/29306139" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20811717", "url": "https://glygen.org/publication/PubMed/20811717", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12692126", "url": "https://glygen.org/publication/PubMed/12692126", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195", "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20230923", "url": "https://glygen.org/publication/PubMed/20230923", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17692050", "url": "https://glygen.org/publication/PubMed/17692050", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19595712", "url": "https://glygen.org/publication/PubMed/19595712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21660950", "url": "https://glygen.org/publication/PubMed/21660950", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21937583", "url": "https://glygen.org/publication/PubMed/21937583", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27105500", "url": "https://glygen.org/publication/PubMed/27105500", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29306139", "url": "https://glygen.org/publication/PubMed/29306139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SLSSPADSYNEGVKLQPQEI", "down_seq": "PPPTANLDRSNDKVYENVTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P27361-1", "kinase_gene_name": "MAPK3", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "20811717", "url": "https://glygen.org/publication/PubMed/20811717" } ], "site_lbl": "Ser910" }, { "kinase_uniprot_canonical_ac": "P28482-1", "kinase_gene_name": "MAPK1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "12692126", "url": "https://glygen.org/publication/PubMed/12692126" }, { "database": "PubMed", "id": "20811717", "url": "https://glygen.org/publication/PubMed/20811717" } ], "site_lbl": "Ser910" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "19369195", "url": "https://glygen.org/publication/PubMed/19369195" }, { "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": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "11160818", "url": "https://glygen.org/publication/PubMed/11160818" }, { "database": "PubMed", "id": "19415658", "url": "https://glygen.org/publication/PubMed/19415658" }, { "database": "PubMed", "id": "20058876", "url": "https://glygen.org/publication/PubMed/20058876" }, { "database": "PubMed", "id": "20230923", "url": "https://glygen.org/publication/PubMed/20230923" }, { "database": "PubMed", "id": "17240116", "url": "https://glygen.org/publication/PubMed/17240116" }, { "database": "PubMed", "id": "17692050", "url": "https://glygen.org/publication/PubMed/17692050" }, { "database": "PubMed", "id": "19595712", "url": "https://glygen.org/publication/PubMed/19595712" }, { "database": "PubMed", "id": "19923420", "url": "https://glygen.org/publication/PubMed/19923420" }, { "database": "PubMed", "id": "21660950", "url": "https://glygen.org/publication/PubMed/21660950" }, { "database": "PubMed", "id": "21937583", "url": "https://glygen.org/publication/PubMed/21937583" }, { "database": "PubMed", "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393" }, { "database": "PubMed", "id": "27105500", "url": "https://glygen.org/publication/PubMed/27105500" }, { "database": "PubMed", "id": "29306139", "url": "https://glygen.org/publication/PubMed/29306139" } ], "site_lbl": "Ser910" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q05397-1.892.892", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q05397-1.914.914", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q05397-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q05397-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q05397-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q05397-1.928.928", "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": 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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.914.914", "start_pos": 914, "end_pos": 914, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "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": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PADSYNEGVKLQPQEISPPP", "down_seq": "ANLDRSNDKVYENVTGLVKA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "17081983", "url": "https://glygen.org/publication/PubMed/17081983" } ], "site_lbl": "Thr914" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q05397-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q05397-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q05397-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q05397-1.925.925", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q05397-1.928.928", "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": "Q05397-1.925.925", "start_pos": 925, "end_pos": 925, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Direct phosphorylation of proliferative and survival pathway proteins by RET.", "journal": "Surgery", "date": "2005", "authors": "Panta GR, Du L, Nwariaku FE, Kim LT", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" } ] }, { "title": "Focal adhesion kinase (FAK) binds RET kinase via its FERM domain, priming a direct and reciprocal RET-FAK transactivation mechanism.", "journal": "The Journal of biological chemistry", "date": "2011", "authors": "Plaza-Menacho I, Morandi A, Mologni L, Boender P, Gambacorti-Passerini C, Magee AI, Hofstra RM, Knowles P, McDonald NQ, Isacke CM", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" } ] }, { "title": "Direct interaction of focal adhesion kinase (FAK) with Met is required for FAK to promote hepatocyte growth factor-induced cell invasion.", "journal": "Molecular and cellular biology", "date": "2006", "authors": "Chen SY, Chen HC", "evidence": [ { "database": "Reactome", "id": "R-HSA-8874081", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8874081" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ] }, { "title": "Site-specific phosphorylation of platelet focal adhesion kinase by low-density lipoprotein.", "journal": "The Biochemical journal", "date": "2003", "authors": "Relou IA, Bax LA, van Rijn HJ, Akkerman JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ] }, { "title": "Integrin-mediated signal transduction linked to Ras pathway by GRB2 binding to focal adhesion kinase.", "journal": "Nature", "date": "1994", "authors": "Schlaepfer DD, Hanks SK, Hunter T, van der Geer P", "evidence": [ { "database": "Reactome", "id": "R-HSA-354194", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-354194" }, { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "7997267", "url": "https://glygen.org/publication/PubMed/7997267" } ] }, { "title": "Evidence for in vivo phosphorylation of the Grb2 SH2-domain binding site on focal adhesion kinase by Src-family protein-tyrosine kinases.", "journal": "Molecular and cellular biology", "date": "1996", "authors": "Schlaepfer DD, Hunter T", "evidence": [ { "database": "iPTMnet", "id": "Q05397-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397-1" } ], "reference": [ { "type": "PubMed", "id": "8816475", "url": "https://glygen.org/publication/PubMed/8816475" } ] }, { "title": "Specific tyrosine phosphorylation of focal adhesion kinase mediated by Fer tyrosine kinase in suspended hepatocytes.", "journal": "Biochimica et biophysica acta", "date": "2009", "authors": "Oh MA, Choi S, Lee MJ, Choi MC, Lee SA, Ko W, Cance WG, Oh ES, Buday L, Kim SH, Lee JW", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ] }, { "title": "Stimulation of human monocytes with macrophage colony-stimulating factor induces a Grb2-mediated association of the focal adhesion kinase pp125FAK and dynamin.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "1995", "authors": "Kharbanda S, Saleem A, Yuan Z, Emoto Y, Prasad KV, Kufe D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "7597091", "url": "https://glygen.org/publication/PubMed/7597091" } ] }, { "title": "Integrin activation and focal complex formation in cardiac hypertrophy.", "journal": "The Journal of biological chemistry", "date": "2000", "authors": "Laser M, Willey CD, Jiang W, Cooper G 4th, Menick DR, Zile MR, Kuppuswamy D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "10958798", "url": "https://glygen.org/publication/PubMed/10958798" } ] }, { "title": "Uniaxial cyclic stretch induces focal adhesion kinase (FAK) tyrosine phosphorylation followed by mitogen-activated protein kinase (MAPK) activation.", "journal": "Biochemical and biophysical research communications", "date": "2001-10-26", "authors": "Wang J G, Miyazu M, Matsushita E, Sokabe M, Naruse K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "11606050", "url": "https://glygen.org/publication/PubMed/11606050" } ] }, { "title": "Focal complex formation in adult cardiomyocytes is accompanied by the activation of beta3 integrin and c-Src.", "journal": "Journal of molecular and cellular cardiology", "date": "2003", "authors": "Willey CD, Balasubramanian S, Rodriguez Rosas MC, Ross RS, Kuppuswamy D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "12788385", "url": "https://glygen.org/publication/PubMed/12788385" } ] }, { "title": "Collagen IV regulates Caco-2 migration and ERK activation via alpha1beta1- and alpha2beta1-integrin-dependent Src kinase activation.", "journal": "American journal of physiology. Gastrointestinal and liver physiology", "date": "2004", "authors": "Sanders MA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14604860", "url": "https://glygen.org/publication/PubMed/14604860" } ] }, { "title": "Ionizing radiation modules of the expression and tyrosine phosphorylation of the focal adhesion-associated proteins focal adhesion kinase (FAK) and its substrates p130cas and paxillin in A549 human lung carcinoma cells in vitro.", "journal": "International journal of radiation biology", "date": "2003", "authors": "Beinke C, Van Beuningen D, Cordes N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "14703945", "url": "https://glygen.org/publication/PubMed/14703945" } ] }, { "title": "Roles played by a subset of integrin signaling molecules in cadherin-based cell-cell adhesion.", "journal": "The Journal of cell biology", "date": "2004", "authors": "Yano H, Mazaki Y, Kurokawa K, Hanks SK, Matsuda M, Sabe H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" } ] }, { "title": "Identification of Src-specific phosphorylation site on focal adhesion kinase: dissection of the role of Src SH2 and catalytic functions and their consequences for tumor cell behavior.", "journal": "Cancer research", "date": "2005", "authors": "Brunton VG, Avizienyte E, Fincham VJ, Serrels B, Metcalf CA 3rd, Sawyer TK, Frame MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" } ] }, { "title": "p130cas but not paxillin is essential for Caco-2 intestinal epithelial cell spreading and migration on collagen IV.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Sanders MA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "15817476", "url": "https://glygen.org/publication/PubMed/15817476" } ] }, { "title": "FAK signaling is critical for ErbB-2/ErbB-3 receptor cooperation for oncogenic transformation and invasion.", "journal": "The Journal of cell biology", "date": "2005-11-07", "authors": "Benlimame Naciba, He Qiang, Jie Su, Xiao Dingzhang, Xu Ying Jie, Loignon Martin, Schlaepfer David D, Alaoui-Jamali Moulay A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754" } ] }, { "title": "Integrin alpha3beta1-dependent activation of FAK/Src regulates Rac1-mediated keratinocyte polarization on laminin-5.", "journal": "The Journal of investigative dermatology", "date": "2007", "authors": "Choma DP, Milano V, Pumiglia KM, DiPersio CM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494" } ] }, { "title": "Analysis of phosphorylation sites on focal adhesion kinase using nanospray liquid chromatography/multiple reaction monitoring mass spectrometry.", "journal": "Rapid communications in mass spectrometry : RCM", "date": "2006", "authors": "Ciccimaro E, Hevko J, Blair IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" } ] }, { "title": "A novel low-molecular weight inhibitor of focal adhesion kinase, TAE226, inhibits glioma growth.", "journal": "Molecular carcinogenesis", "date": "2007", "authors": "Shi Q, Hjelmeland AB, Keir ST, Song L, Wickman S, Jackson D, Ohmori O, Bigner DD, Friedman HS, Rich JN", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439" } ] }, { "title": "Tumor necrosis factor-alpha stimulates focal adhesion kinase activity required for mitogen-activated kinase-associated interleukin 6 expression.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Schlaepfer DD, Hou S, Lim ST, Tomar A, Yu H, Lim Y, Hanson DA, Uryu SA, Molina J, Mitra SK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17438336", "url": "https://glygen.org/publication/PubMed/17438336" } ] }, { "title": "Proinvasive activity of BMP-7 through SMAD4/src-independent and ERK/Rac/JNK-dependent signaling pathways in colon cancer cells.", "journal": "Cellular signalling", "date": "2007", "authors": "Grijelmo C, Rodrigue C, Svrcek M, Bruyneel E, Hendrix A, de Wever O, Gespach C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "17478078", "url": "https://glygen.org/publication/PubMed/17478078" } ] }, { "title": "MAP-kinase activity necessary for TGFbeta1-stimulated mesangial cell type I collagen expression requires adhesion-dependent phosphorylation of FAK tyrosine 397.", "journal": "Journal of cell science", "date": "2007", "authors": "Hayashida T, Wu MH, Pierce A, Poncelet AC, Varga J, Schnaper HW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18032789", "url": "https://glygen.org/publication/PubMed/18032789" } ] }, { "title": "FAK-mediated activation of ERK for eosinophil migration: a novel mechanism for infection-induced allergic inflammation.", "journal": "International immunology", "date": "2008", "authors": "Cheung PF, Wong CK, Ip WK, Lam CW", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18182379", "url": "https://glygen.org/publication/PubMed/18182379" } ] }, { "title": "Inhibitory role of focal adhesion kinase on anoikis in the lung cancer cell A549.", "journal": "Cell biology international", "date": "2008", "authors": "Liu G, Meng X, Jin Y, Bai J, Zhao Y, Cui X, Chen F, Fu S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694" } ] }, { "title": "Involvement of focal adhesion kinase in cellular invasion of head and neck squamous cell carcinomas via regulation of MMP-2 expression.", "journal": "British journal of cancer", "date": "2008-04-08", "authors": "Canel M, Secades P, Garz\u00f3n-Arango M, Allonca E, Suarez C, Serrels A, Frame Mc, Brunton V, Chiara M-D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846" } ] }, { "title": "Repetitive deformation activates Src-independent FAK-dependent ERK motogenic signals in human Caco-2 intestinal epithelial cells.", "journal": "American journal of physiology. Cell physiology", "date": "2008", "authors": "Chaturvedi LS, Gayer CP, Marsh HM, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18400991", "url": "https://glygen.org/publication/PubMed/18400991" } ] }, { "title": "Early adhesion induces interaction of FAK and Fyn in lipid domains and activates raft-dependent Akt signaling in SW480 colon cancer cells.", "journal": "Biochimica et biophysica acta", "date": "2008", "authors": "Baillat G, Siret C, Delamarre E, Luis J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444" } ] }, { "title": "Regulation of focal adhesion turnover by ErbB signalling in invasive breast cancer cells.", "journal": "British journal of cancer", "date": "2009-02-24", "authors": "Xu Y, Benlimame N, Su J, He Q, Alaoui-Jamali M A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626" } ] }, { "title": "Characterisation of fibronectin-mediated FAK signalling pathways in lung cancer cell migration and invasion.", "journal": "British journal of cancer", "date": "2009", "authors": "Meng XN, Jin Y, Yu Y, Bai J, Liu GY, Zhu J, Zhao YZ, Wang Z, Chen F, Lee KY, Fu SB", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240" } ] }, { "title": "Endothelial barrier protection by FTY720 under hyperglycemic condition: involvement of focal adhesion kinase, small GTPases, and adherens junction proteins.", "journal": "American journal of physiology. Cell physiology", "date": "2009", "authors": "Sarai K, Shikata K, Shikata Y, Omori K, Watanabe N, Sasaki M, Nishishita S, Wada J, Goda N, Kataoka N, Makino H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053" } ] }, { "title": "Therapeutic targeting of the focal adhesion complex prevents oncogenic TGF-beta signaling and metastasis.", "journal": "Breast cancer research : BCR", "date": "2009", "authors": "Wendt MK, Schiemann WP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433" } ] }, { "title": "Matrix density-induced mechanoregulation of breast cell phenotype, signaling and gene expression through a FAK-ERK linkage.", "journal": "Oncogene", "date": "2009", "authors": "Provenzano PP, Inman DR, Eliceiri KW, Keely PJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19826415", "url": "https://glygen.org/publication/PubMed/19826415" } ] }, { "title": "Stretch activates human myometrium via ERK, caldesmon and focal adhesion signaling.", "journal": "PloS one", "date": "2009", "authors": "Li Y, Reznichenko M, Tribe RM, Hess PE, Taggart M, Kim H, DeGnore JP, Gangopadhyay S, Morgan KG", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "19834610", "url": "https://glygen.org/publication/PubMed/19834610" } ] }, { "title": "Preliminary crystallographic characterization of the Grb2 SH2 domain in complex with a FAK-derived phosphotyrosyl peptide.", "journal": "Acta crystallographica. Section F, Structural biology and crystallization communications", "date": "2010", "authors": "Chen HH, Chen CW, Chang YY, Shen TL, Hsu CH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20124721", "url": "https://glygen.org/publication/PubMed/20124721" } ] }, { "title": "Hydrogen peroxide activates focal adhesion kinase and c-Src by a phosphatidylinositol 3 kinase-dependent mechanism and promotes cell migration in Caco-2 cell monolayers.", "journal": "American journal of physiology. Gastrointestinal and liver physiology", "date": "2010", "authors": "Basuroy S, Dunagan M, Sheth P, Seth A, Rao RK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826" } ] }, { "title": "Dual targeting of EphA2 and ER restores tamoxifen sensitivity in ER/EphA2-positive breast cancer.", "journal": "Breast cancer research and treatment", "date": "2011-06", "authors": "G\u00f6kmen-Polar Yesim, Toroni Rachel A, Hocevar Barbara A, Badve Sunil, Zhao Qianqian, Shen Changyu, Bruckheimer Elizabeth, Kinch Michael S, Miller Kathy D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20602165", "url": "https://glygen.org/publication/PubMed/20602165" } ] }, { "title": "Dasatinib reduces FAK phosphorylation increasing the effects of RPI-1 inhibition in a RET/PTC1-expressing cell line.", "journal": "Molecular cancer", "date": "2010", "authors": "Caccia D, Micciche F, Cassinelli G, Mondellini P, Casalini P, Bongarzone I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" } ] }, { "title": "ILK mediates the effects of strain on intestinal epithelial wound closure.", "journal": "American journal of physiology. Cell physiology", "date": "2011", "authors": "Yuan L, Sanders MA, Basson MD", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641" } ] }, { "title": "Androgen-induced cell migration: role of androgen receptor/filamin A association.", "journal": "PloS one", "date": "2011", "authors": "Castoria G, D'Amato L, Ciociola A, Giovannelli P, Giraldi T, Sepe L, Paolella G, Barone MV, Migliaccio A, Auricchio F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21359179", "url": "https://glygen.org/publication/PubMed/21359179" } ] }, { "title": "Suppression of E-cadherin function drives the early stages of Ras-induced squamous cell carcinoma through upregulation of FAK and Src.", "journal": "The Journal of investigative dermatology", "date": "2011", "authors": "Alt-Holland A, Sowalsky AG, Szwec-Levin Y, Shamis Y, Hatch H, Feig LA, Garlick JA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" } ] }, { "title": "Kisspeptin-10 inhibits cell migration in vitro via a receptor-GSK3 beta-FAK feedback loop in HTR8SVneo cells.", "journal": "Placenta", "date": "2012", "authors": "Roseweir AK, Katz AA, Millar RP", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22349353", "url": "https://glygen.org/publication/PubMed/22349353" } ] }, { "title": "Post-radiation increase in VEGF enhances glioma cell motility in vitro.", "journal": "Radiation oncology (London, England)", "date": "2012", "authors": "Kil WJ, Tofilon PJ, Camphausen K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22356893", "url": "https://glygen.org/publication/PubMed/22356893" } ] }, { "title": "uPAR and cathepsin B knockdown inhibits radiation-induced PKC integrated integrin signaling to the cytoskeleton of glioma-initiating cells.", "journal": "International journal of oncology", "date": "2012", "authors": "Alapati K, Gopinath S, Malla RR, Dasari VR, Rao JS", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22641287", "url": "https://glygen.org/publication/PubMed/22641287" } ] }, { "title": "Adhesion-mediated cytoskeletal remodeling is controlled by the direct scaffolding of Src from FAK complexes to lipid rafts by SSeCKS/AKAP12.", "journal": "Oncogene", "date": "2013", "authors": "Su B, Gao L, Meng F, Guo LW, Rothschild J, Gelman IH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22710722", "url": "https://glygen.org/publication/PubMed/22710722" } ] }, { "title": "Integrin beta5 contributes to the tumorigenic potential of breast cancer cells through the Src-FAK and MEK-ERK signaling pathways.", "journal": "Oncogene", "date": "2013", "authors": "Bianchi-Smiraglia A, Paesante S, Bakin AV", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793" } ] }, { "title": "Mda-9/syntenin promotes human brain glioma migration through focal adhesion kinase (FAK)-JNK and FAK-AKT signaling.", "journal": "Asian Pacific journal of cancer prevention : APJCP", "date": "2012", "authors": "Zhong D, Ran JH, Tang WY, Zhang XD, Tan Y, Chen GJ, Li XS, Yan Y", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" } ] }, { "title": "Rap1 can bypass the FAK-Src-Paxillin cascade to induce cell spreading and focal adhesion formation.", "journal": "PloS one", "date": "2012", "authors": "Ross SH, Spanjaard E, Post A, Vliem MJ, Kristyanto H, Bos JL, de Rooij J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" } ] }, { "title": "Stiff collagen matrices increase tumorigenic prolactin signaling in breast cancer cells.", "journal": "The Journal of biological chemistry", "date": "2013", "authors": "Barcus CE, Keely PJ, Eliceiri KW, Schuler LA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23530035", "url": "https://glygen.org/publication/PubMed/23530035" } ] }, { "title": "Identification of methyl violet 2B as a novel blocker of focal adhesion kinase signaling pathway in cancer cells.", "journal": "Biochemical and biophysical research communications", "date": "2013", "authors": "Kim H, Kim ND, Lee J, Han G, Sim T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23817042", "url": "https://glygen.org/publication/PubMed/23817042" } ] }, { "title": "Inhibition of Src activation with cardiotoxin III blocks migration and invasion of MDA-MB-231 cells.", "journal": "Toxicon : official journal of the International Society on Toxinology", "date": "2013-11", "authors": "Tsai Pei-Chien, Chu Chiao-Lun, Chiu Chien-Chih, Chang Long-Sen, Lin Shinne-Ren", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586" } ] }, { "title": "Binding of alphavbeta1 and alphavbeta6 integrins to tenascin-C induces epithelial-mesenchymal transition-like change of breast cancer cells.", "journal": "Oncogenesis", "date": "2013", "authors": "Katoh D, Nagaharu K, Shimojo N, Hanamura N, Yamashita M, Kozuka Y, Imanaka-Yoshida K, Yoshida T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "23958855", "url": "https://glygen.org/publication/PubMed/23958855" } ] }, { "title": "Optimising parameters for the differentiation of SH-SY5Y cells to study cell adhesion and cell migration.", "journal": "BMC research notes", "date": "2013-09-11", "authors": "Dwane Susan, Durack Edel, Kiely Patrick A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24025096", "url": "https://glygen.org/publication/PubMed/24025096" } ] }, { "title": "CD13 promotes mesenchymal stem cell-mediated regeneration of ischemic muscle.", "journal": "Frontiers in physiology", "date": "2014", "authors": "Rahman MM, Subramani J, Ghosh M, Denninger JK, Takeda K, Fong GH, Carlson ME, Shapiro LH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24409152", "url": "https://glygen.org/publication/PubMed/24409152" } ] }, { "title": "The 2-pore domain potassium channel TREK-1 regulates stretch-induced detachment of alveolar epithelial cells.", "journal": "PloS one", "date": "2014", "authors": "Roan E, Waters CM, Teng B, Ghosh M, Schwingshackl A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24586773", "url": "https://glygen.org/publication/PubMed/24586773" } ] }, { "title": "Altering FAK-paxillin interactions reduces adhesion, migration and invasion processes.", "journal": "PloS one", "date": "2014", "authors": "Deramaudt Th\u00e9r\u00e8se B, Dujardin Denis, Noulet Fanny, Martin Sophie, Vauchelles Romain, Takeda Ken, Rond\u00e9 Philippe", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" } ] }, { "title": "Biglycan enhances gastric cancer invasion by activating FAK signaling pathway.", "journal": "Oncotarget", "date": "2014", "authors": "Hu L, Duan YT, Li JF, Su LP, Yan M, Zhu ZG, Liu BY, Yang QM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" } ] }, { "title": "The marine-derived sipholenol A-4-O-3',4'-dichlorobenzoate inhibits breast cancer growth and motility in vitro and in vivo through the suppression of Brk and FAK signaling.", "journal": "Marine drugs", "date": "2014", "authors": "Akl MR, Foudah AI, Ebrahim HY, Meyer SA, El Sayed KA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" } ] }, { "title": "The Polycomb group protein RING1B is overexpressed in ductal breast carcinoma and is required to sustain FAK steady state levels in breast cancer epithelial cells.", "journal": "Oncotarget", "date": "2014", "authors": "Bosch A, Panoutsopoulou K, Corominas JM, Gimeno R, Moreno-Bueno G, Martin-Caballero J, Morales S, Lobato T, Martinez-Romero C, Farias EF, Mayol X, Cano A, Hernandez-Munoz I", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24742605", "url": "https://glygen.org/publication/PubMed/24742605" } ] }, { "title": "Maternal embryonic leucine zipper kinase enhances gastric cancer progression via the FAK/Paxillin pathway.", "journal": "Molecular cancer", "date": "2014", "authors": "Du T, Qu Y, Li J, Li H, Su L, Zhou Q, Yan M, Li C, Zhu Z, Liu B", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" } ] }, { "title": "Nanometer scale titanium surface texturing are detected by signaling pathways involving transient FAK and Src activations.", "journal": "PloS one", "date": "2014", "authors": "Zambuzzi Willian F, Bonfante Estevam A, Jimbo Ryo, Hayashi Mariko, Andersson Martin, Alves Gutemberg, Takamori Esther R, Beltr\u00e3o Paulo J, Coelho Paulo G, Granjeiro Jos\u00e9 M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "24999733", "url": "https://glygen.org/publication/PubMed/24999733" } ] }, { "title": "Inhibition of smooth muscle force generation by focal adhesion kinase inhibitors in the hyperplastic human prostate.", "journal": "American journal of physiology. Renal physiology", "date": "2014", "authors": "Kunit T, Gratzke C, Schreiber A, Strittmatter F, Waidelich R, Rutz B, Loidl W, Andersson KE, Stief CG, Hennenberg M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25056351", "url": "https://glygen.org/publication/PubMed/25056351" } ] }, { "title": "Overcoming EMT-associated resistance to anti-cancer drugs via Src/FAK pathway inhibition.", "journal": "Oncotarget", "date": "2014", "authors": "Wilson C, Nicholes K, Bustos D, Lin E, Song Q, Stephan JP, Kirkpatrick DS, Settleman J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" } ] }, { "title": "A novel aminothiazole KY-05009 with potential to inhibit Traf2- and Nck-interacting kinase (TNIK) attenuates TGF-beta1-mediated epithelial-to-mesenchymal transition in human lung adenocarcinoma A549 cells.", "journal": "PloS one", "date": "2014", "authors": "Kim J, Moon SH, Kim BT, Chae CH, Lee JY, Kim SH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25337707", "url": "https://glygen.org/publication/PubMed/25337707" } ] }, { "title": "Loss of anchorage primarily induces non-apoptotic cell death in a human mammary epithelial cell line under atypical focal adhesion kinase signaling.", "journal": "Cell death & disease", "date": "2015-01-22", "authors": "Ishikawa F, Ushida K, Mori K, Shibanuma M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393" } ] }, { "title": "Ruthenium polypyridyl complex inhibits growth and metastasis of breast cancer cells by suppressing FAK signaling with enhancement of TRAIL-induced apoptosis.", "journal": "Scientific reports", "date": "2015", "authors": "Cao W, Zheng W, Chen T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" } ] }, { "title": "Inactivation of Src-to-ezrin pathway: a possible mechanism in the ouabain-mediated inhibition of A549 cell migration.", "journal": "BioMed research international", "date": "2015", "authors": "Shin HK, Ryu BJ, Choi SW, Kim SH, Lee K", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25866790", "url": "https://glygen.org/publication/PubMed/25866790" } ] }, { "title": "Pinocembrin suppresses TGF-\u03b21-induced epithelial-mesenchymal transition and metastasis of human Y-79 retinoblastoma cells through inactivating \u03b1v\u03b23 integrin/FAK/p38\u03b1 signaling pathway.", "journal": "Cell & bioscience", "date": "2014", "authors": "Chen Kun-Shiang, Shi Ming-Der, Chien Chi-Sheng, Shih Yuan-Wei", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790" } ] }, { "title": "Novel anticancer agent, SQAP, binds to focal adhesion kinase and modulates its activity.", "journal": "Scientific reports", "date": "2015", "authors": "Izaguirre-Carbonell J, Kawakubo H, Murata H, Tanabe A, Takeuchi T, Kusayanagi T, Tsukuda S, Hirakawa T, Iwabata K, Kanai Y, Ohta K, Miura M, Sakaguchi K, Matsunaga S, Sahara H, Kamisuki S, Sugawara F", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26456697", "url": "https://glygen.org/publication/PubMed/26456697" } ] }, { "title": "Growth-stimulatory activity of TIMP-2 is mediated through c-Src activation followed by activation of FAK, PI3-kinase/AKT, and ERK1/2 independent of MMP inhibition in lung adenocarcinoma cells.", "journal": "Oncotarget", "date": "2015", "authors": "Kim HIe, Lee HS, Kim TH, Lee JS, Lee ST, Lee SJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26556867", "url": "https://glygen.org/publication/PubMed/26556867" } ] }, { "title": "NDN is an imprinted tumor suppressor gene that is downregulated in ovarian cancers through genetic and epigenetic mechanisms.", "journal": "Oncotarget", "date": "2016", "authors": "Yang H, Das P, Yu Y, Mao W, Wang Y, Baggerly K, Wang Y, Marquez RT, Bedi A, Liu J, Fishman D, Lu Z, Bast RC Jr", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "26689988", "url": "https://glygen.org/publication/PubMed/26689988" } ] }, { "title": "Sulfatide interacts with and activates integrin \u03b1V\u03b23 in human hepatocellular carcinoma cells.", "journal": "Oncotarget", "date": "2016-06-14", "authors": "Wang Rong, Qi Bing, Dong Yi Wei, Cai Qian Qian, Deng Nian Hui, Chen Qi, Li Chao, Jin Yu Tong, Wu Xing Zhong", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276" } ] }, { "title": "HER2 reduces breast cancer radiosensitivity by activating focal adhesion kinase in vitro and in vivo.", "journal": "Oncotarget", "date": "2016", "authors": "Hou J, Zhou Z, Chen X, Zhao R, Yang Z, Wei N, Ni Q, Feng Y, Yu X, Ma J, Guo X", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256" } ] }, { "title": "MUC13 interaction with receptor tyrosine kinase HER2 drives pancreatic ductal adenocarcinoma progression.", "journal": "Oncogene", "date": "2017", "authors": "Khan S, Sikander M, Ebeling MC, Ganju A, Kumari S, Yallapu MM, Hafeez BB, Ise T, Nagata S, Zafar N, Behrman SW, Wan JY, Ghimire HM, Sahay P, Pradhan P, Chauhan SC, Jaggi M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27321183", "url": "https://glygen.org/publication/PubMed/27321183" } ] }, { "title": "Prolactin signaling through focal adhesion complexes is amplified by stiff extracellular matrices in breast cancer cells.", "journal": "Oncotarget", "date": "2016-07-26", "authors": "Barcus Craig E, Keely Patricia J, Eliceiri Kevin W, Schuler Linda A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27344177", "url": "https://glygen.org/publication/PubMed/27344177" } ] }, { "title": "Neutral endopeptidase (NEP) is differentially involved in biological activities and cell signaling of colon cancer cell lines derived from various stages of tumor development.", "journal": "Tumour biology : the journal of the International Society for Oncodevelopmental Biology and Medicine", "date": "2016", "authors": "Mizerska-Kowalska M, Bojarska-Junak A, Jakubowicz-Gil J, Kandefer-Szerszen M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27460083", "url": "https://glygen.org/publication/PubMed/27460083" } ] }, { "title": "MIEN1 drives breast tumor cell migration by regulating cytoskeletal-focal adhesion dynamics.", "journal": "Oncotarget", "date": "2016", "authors": "Kpetemey M, Chaudhary P, Van Treuren T, Vishwanatha JK", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27462783", "url": "https://glygen.org/publication/PubMed/27462783" } ] }, { "title": "The metastasis suppressor CD82/KAI1 inhibits fibronectin adhesion-induced epithelial-to-mesenchymal transition in prostate cancer cells by repressing the associated integrin signaling.", "journal": "Oncotarget", "date": "2017", "authors": "Lee J, Byun HJ, Lee MS, Jin YJ, Jeoung D, Kim YM, Lee H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27926483", "url": "https://glygen.org/publication/PubMed/27926483" } ] }, { "title": "Induction of Integrin Signaling by Steroid Sulfatase in Human Cervical Cancer Cells.", "journal": "Biomolecules & therapeutics", "date": "2017", "authors": "Ye DJ, Kwon YJ, Shin S, Baek HS, Shin DW, Chun YJ", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27956712", "url": "https://glygen.org/publication/PubMed/27956712" } ] }, { "title": "Aeroallergen Der p 2 promotes motility of human non-small cell lung cancer cells via toll-like receptor-mediated up-regulation of urokinase-type plasminogen activator and integrin/focal adhesion kinase signaling.", "journal": "Oncotarget", "date": "2017", "authors": "Lin CH, Lin HH, Kuo CY, Kao SH", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28076322", "url": "https://glygen.org/publication/PubMed/28076322" } ] }, { "title": "DCYTB is a predictor of outcome in breast cancer that functions via iron-independent mechanisms.", "journal": "Breast cancer research : BCR", "date": "2017", "authors": "Lemler DJ, Lynch ML, Tesfay L, Deng Z, Paul BT, Wang X, Hegde P, Manz DH, Torti SV, Torti FM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28270217", "url": "https://glygen.org/publication/PubMed/28270217" } ] }, { "title": "TRIB1 promotes colorectal cancer cell migration and invasion through activation MMP-2 via FAK/Src and ERK pathways.", "journal": "Oncotarget", "date": "2017-07-18", "authors": "Wang Yuhui, Wu Nan, Pang Bo, Tong Dandan, Sun Donglin, Sun Haiming, Zhang Chunyu, Sun Wenjing, Meng Xiangning, Bai Jing, Chen Feng, Geng Jingshu, Fu Songbin, Jin Yan", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28624785", "url": "https://glygen.org/publication/PubMed/28624785" } ] }, { "title": "Lasp2 enhances tumor invasion via facilitating phosphorylation of FAK and predicts poor overall survival of non-small cell lung cancer patients.", "journal": "Molecular carcinogenesis", "date": "2017", "authors": "Zhang X, Cai L, Zhou H, Liu Y, Fan C, Wang L, Li A, Miao Y, Li Q, Qiu X, Wang E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28667800", "url": "https://glygen.org/publication/PubMed/28667800" } ] }, { "title": "Substrate stiffness governs the initiation of B cell activation by the concerted signaling of PKCbeta and focal adhesion kinase.", "journal": "eLife", "date": "2017", "authors": "Shaheen S, Wan Z, Li Z, Chau A, Li X, Zhang S, Liu Y, Yi J, Zeng Y, Wang J, Chen X, Xu L, Chen W, Wang F, Lu Y, Zheng W, Shi Y, Sun X, Li Z, Xiong C, Liu W", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28755662", "url": "https://glygen.org/publication/PubMed/28755662" } ] }, { "title": "Enhanced efficacy of AKT and FAK kinase combined inhibition in squamous cell lung carcinomas with stable reduction in PTEN.", "journal": "Oncotarget", "date": "2017", "authors": "Cavazzoni A, La Monica S, Alfieri R, Ravelli A, Van Der Steen N, Sciarrillo R, Madeddu D, Lagrasta CAM, Quaini F, Bonelli M, Fumarola C, Cretella D, Digiacomo G, Tiseo M, Peters GJ, Ardizzoni A, Petronini PG, Giovannetti E", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "28881794", "url": "https://glygen.org/publication/PubMed/28881794" } ] }, { "title": "The activation of SRC family kinases and focal adhesion kinase with the loss of the amplified, mutated EGFR gene contributes to the resistance to afatinib, erlotinib and osimertinib in human lung cancer cells.", "journal": "Oncotarget", "date": "2017", "authors": "Murakami Y, Sonoda K, Abe H, Watari K, Kusakabe D, Azuma K, Kawahara A, Akiba J, Oneyama C, Pachter JA, Sakai K, Nishio K, Kuwano M, Ono M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" } ] }, { "title": "Src SUMOylation Inhibits Tumor Growth Via Decreasing FAK Y925 Phosphorylation.", "journal": "Neoplasia (New York, N.Y.)", "date": "2017-12", "authors": "Wang Jing, Deng Rong, Cui Nan, Zhang Hailong, Liu Tianqi, Dou Jinzhuo, Zhao Xian, Chen Ran, Wang Yanli, Yu Jianxiu, Huang Jian", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29069627", "url": "https://glygen.org/publication/PubMed/29069627" } ] }, { "title": "Targeted inhibition of Janus kinases abates interfon gamma-induced invasive behaviour of fibroblast-like synoviocytes.", "journal": "Rheumatology (Oxford, England)", "date": "2018-03-01", "authors": "Karonitsch Thomas, Beckmann Denise, Dalwigk Karolina, Niederreiter Birgit, Studenic Paul, Byrne Ruth A, Holinka Johannes, Sevelda Florian, Korb-Pap Adelheid, Steiner G\u00fcnter, Smolen Josef S, Pap Thomas, Kiener Hans P", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29228301", "url": "https://glygen.org/publication/PubMed/29228301" } ] }, { "title": "Focal adhesion kinases in head and neck squamous cell carcinoma.", "journal": "Journal of oral pathology & medicine : official publication of the International Association of Oral Pathologists and the American Academy of Oral Pathology", "date": "2018", "authors": "Flores APC, Dias KB, Hildebrand LC, Oliveira MG, Lamers ML, Sant'Ana Filho M", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29292531", "url": "https://glygen.org/publication/PubMed/29292531" } ] }, { "title": "Molecular mechanism of action and potential biomarkers of growth inhibition of synergistic combination of afatinib and dasatinib against gefitinib-resistant non-small cell lung cancer cells.", "journal": "Oncotarget", "date": "2018", "authors": "Wang M, Yuang-Chi Chang A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29662665", "url": "https://glygen.org/publication/PubMed/29662665" } ] }, { "title": "RXRalpha provokes tumor suppression through p53/p21/p16 and PI3K-AKT signaling pathways during stem cell differentiation and in cancer cells.", "journal": "Cell death & disease", "date": "2018", "authors": "Zhang R, Li H, Zhang S, Zhang Y, Wang N, Zhou H, He H, Hu G, Zhang TC, Ma W", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29748541", "url": "https://glygen.org/publication/PubMed/29748541" } ] }, { "title": "Extracellular gamma-synuclein promotes tumor cell motility by activating beta1 integrin-focal adhesion kinase signaling pathway and increasing matrix metalloproteinase-24, -2 protein secretion.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2018", "authors": "Liu C, Qu L, Zhao C, Shou C", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29903032", "url": "https://glygen.org/publication/PubMed/29903032" } ] }, { "title": "Cytotoxic activity of Shp2 inhibitor fumosorinone in human cancer cells.", "journal": "Oncology letters", "date": "2018", "authors": "Chen C, Xue T, Fan P, Meng L, Wei J, Luo D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374" } ] }, { "title": "ZIP9 but not the androgen receptor mediates testosterone-induced migratory activity of metastatic prostate cancer cells.", "journal": "Biochimica et biophysica acta. Molecular cell research", "date": "2018", "authors": "Bulldan A, Bartsch JW, Konrad L, Scheiner-Bobis G", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30262433", "url": "https://glygen.org/publication/PubMed/30262433" } ] }, { "title": "Suppression of lung cancer progression by isoliquiritigenin through its metabolite 2, 4, 2', 4'-Tetrahydroxychalcone.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2018", "authors": "Chen C, Shenoy AK, Padia R, Fang D, Jing Q, Yang P, Su SB, Huang S", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30285892", "url": "https://glygen.org/publication/PubMed/30285892" } ] }, { "title": "Bivalent Ligand UDCA-LPE Inhibits Pro-Fibrogenic Integrin Signalling by Inducing Lipid Raft-Mediated Internalization.", "journal": "International journal of molecular sciences", "date": "2018", "authors": "Su J, Gan-Schreier H, Goeppert B, Chamulitrat W, Stremmel W, Pathil A", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" } ] }, { "title": "FAM129B promoted tumor invasion and proliferation via facilitating the phosphorylation of FAK signaling and associated with adverse clinical outcome of non-small cell lung cancer patients.", "journal": "OncoTargets and therapy", "date": "2018", "authors": "Zhou X, Yang F, Zhang Q, Miao Y, Hu X, Li A, Hou G, Wang Q, Kang J", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362" } ] }, { "title": "The increased adhesion of tumor cells to endothelial cells after irradiation can be reduced by FAK-inhibition.", "journal": "Radiation oncology (London, England)", "date": "2019", "authors": "Nguemgo Kouam P, Buhler H, Hero T, Adamietz IA", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "30717801", "url": "https://glygen.org/publication/PubMed/30717801" } ] }, { "title": "Afatinib and Temozolomide combination inhibits tumorigenesis by targeting EGFRvIII-cMet signaling in glioblastoma cells.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2019", "authors": "Vengoji R, Macha MA, Nimmakayala RK, Rachagani S, Siddiqui JA, Mallya K, Gorantla S, Jain M, Ponnusamy MP, Batra SK, Shonka N", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31215502", "url": "https://glygen.org/publication/PubMed/31215502" } ] }, { "title": "Identification of new binding proteins of focal adhesion kinase using immunoprecipitation and mass spectrometry.", "journal": "Scientific reports", "date": "2019-09-09", "authors": "Nguyen Binh Thanh, Pyun Jae-Chul, Lee Sang-Guk, Kang Min-Jung", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "31501460", "url": "https://glygen.org/publication/PubMed/31501460" } ] }, { "title": "Raftlin is recruited by neuropilin-1 to the activated VEGFR2 complex to control proangiogenic signaling.", "journal": "Angiogenesis", "date": "2020", "authors": "Bayliss AL, Sundararaman A, Granet C, Mellor H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611" } ] }, { "title": "Effect of Sugars on Chlamydia trachomatis Infectivity.", "journal": "Pathogens (Basel, Switzerland)", "date": "2020-04-17", "authors": "Marziali Giacomo, Marangoni Antonella, Foschi Claudio, Re Maria Carla, Calonghi Natalia", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32316668", "url": "https://glygen.org/publication/PubMed/32316668" } ] }, { "title": "EPH receptor B2 stimulates human monocyte adhesion and migration independently of its EphrinB ligands.", "journal": "Journal of leukocyte biology", "date": "2020", "authors": "Vreeken D, Bruikman CS, Cox SML, Zhang H, Lalai R, Koudijs A, van Zonneveld AJ, Hovingh GK, van Gils JM", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32337793", "url": "https://glygen.org/publication/PubMed/32337793" } ] }, { "title": "The Membrane Protein Sortilin Can Be Targeted to Inhibit Pancreatic Cancer Cell Invasion.", "journal": "The American journal of pathology", "date": "2020", "authors": "Gao F, Griffin N, Faulkner S, Li X, King SJ, Jobling P, Denham JW, Jiang CC, Hondermarck H", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32526166", "url": "https://glygen.org/publication/PubMed/32526166" } ] }, { "title": "Structure-Based Virtual Screening, Synthesis and Biological Evaluation of Potential FAK-FAT Domain Inhibitors for Treatment of Metastatic Cancer.", "journal": "Molecules (Basel, Switzerland)", "date": "2020-07-31", "authors": "Kandil Sahar B, Jones Samuel R, Smith Sonia, Hiscox Stephen E, Westwell Andrew D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "32751931", "url": "https://glygen.org/publication/PubMed/32751931" } ] }, { "title": "Targeting SRC Kinase Signaling in Pancreatic Cancer Stem Cells.", "journal": "International journal of molecular sciences", "date": "2020-10-09", "authors": "Alcal\u00e1 Sonia, Mayoral-Varo V\u00edctor, Ruiz-Ca\u00f1as Laura, L\u00f3pez-Gil Juan Carlos, Heeschen Christopher, Mart\u00edn-P\u00e9rez Jorge, Sainz Bruno", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33050159", "url": "https://glygen.org/publication/PubMed/33050159" } ] }, { "title": "C1GALT1 high expression is associated with poor survival of patients with pancreatic ductal adenocarcinoma and promotes cell invasiveness through integrin alphav.", "journal": "Oncogene", "date": "2021", "authors": "Kuo TC, Wu MH, Yang SH, Chen ST, Hsu TW, Jhuang JY, Liao YY, Tien YW, Huang MC", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33420364", "url": "https://glygen.org/publication/PubMed/33420364" } ] }, { "title": "Molecular Basis of LH Action on Breast Cancer Cell Migration and Invasion via Kinase and Scaffold Proteins.", "journal": "Frontiers in cell and developmental biology", "date": "2020", "authors": "Mondaca Joselina Magali, Uzair Ivonne Denise, Castro Guijarro Ana Carla, Flamini Marina In\u00e9s, Sanchez Angel Matias", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" } ] }, { "title": "Focal adhesion kinase inhibition synergizes with nab-paclitaxel to target pancreatic ductal adenocarcinoma.", "journal": "Journal of experimental & clinical cancer research : CR", "date": "2021-03-09", "authors": "Le Large T Y S, Bijlsma M F, El Hassouni B, Mantini G, Lagerweij T, Henneman A A, Funel N, Kok B, Pham T V, de Haas R, Morelli L, Knol J C, Piersma S R, Kazemier G, van Laarhoven H W M, Giovannetti E, Jimenez C R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "33750427", "url": "https://glygen.org/publication/PubMed/33750427" } ] }, { "title": "Discovery of novel chloropyramine-cinnamic acid hybrids as potential FAK inhibitors for intervention of metastatic triple-negative breast cancer.", "journal": "Bioorganic & medicinal chemistry", "date": "2022-07-15", "authors": "Yang Fei, Xu Kangping, Zhang Sha, Zhang Jinlin, Qiu Yaoren, Luo Jin, Tan Guishan, Zou Zhenxing, Wang Wenxuan, Kang Fenghua", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35569251", "url": "https://glygen.org/publication/PubMed/35569251" } ] }, { "title": "Tyrosine Phosphorylation Profiling Revealed the Signaling Network Characteristics of CAMKK2 in Gastric Adenocarcinoma.", "journal": "Frontiers in genetics", "date": "2022", "authors": "Najar Mohd Altaf, Arefian Mohammad, Sidransky David, Gowda Harsha, Prasad T S Keshava, Modi Prashant Kumar, Chatterjee Aditi", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35646067", "url": "https://glygen.org/publication/PubMed/35646067" } ] }, { "title": "SPARC Induces E-Cadherin Repression and Enhances Cell Migration through Integrin \u03b1v\u03b23 and the Transcription Factor ZEB1 in Prostate Cancer Cells.", "journal": "International journal of molecular sciences", "date": "2022-05-24", "authors": "L\u00f3pez-Moncada Fernanda, Torres Mar\u00eda Jos\u00e9, Lavanderos Boris, Cerda Oscar, Castell\u00f3n Enrique A, Contreras H\u00e9ctor R", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35682554", "url": "https://glygen.org/publication/PubMed/35682554" } ] }, { "title": "RIOK3 promotes pancreatic ductal adenocarcinoma cell invasion and metastasis by stabilizing FAK.", "journal": "Heliyon", "date": "2022-08", "authors": "Xu Mengyuan, Fang Lei, Guo Xin, Qin Henan, Sun Rui, Ning Zhen, Wang Aman", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "35982848", "url": "https://glygen.org/publication/PubMed/35982848" } ] }, { "title": "ZINC40099027 promotes monolayer circular defect closure by a novel pathway involving cytosolic activation of focal adhesion kinase and downstream paxillin and ERK1/2.", "journal": "Cell and tissue research", "date": "2022-11", "authors": "Oncel Sema, Basson Marc D", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "36001146", "url": "https://glygen.org/publication/PubMed/36001146" } ] }, { "title": "Integrin-mediated activation of MAP kinase is independent of FAK: evidence for dual integrin signaling pathways in fibroblasts.", "journal": "The Journal of cell biology", "date": "1997", "authors": "Lin TH, Aplin AE, Shen Y, Chen Q, Schaller M, Romer L, Aukhil I, Juliano RL", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9087451", "url": "https://glygen.org/publication/PubMed/9087451" } ] }, { "title": "Focal adhesion kinase overexpression enhances ras-dependent integrin signaling to ERK2/mitogen-activated protein kinase through interactions with and activation of c-Src.", "journal": "The Journal of biological chemistry", "date": "1997", "authors": "Schlaepfer DD, Hunter T", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "9148935", "url": "https://glygen.org/publication/PubMed/9148935" } ] } ], "crossref": [ { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730", "database": "PubMed", "categories": [ "Other" ] }, { "id": "7997267", "url": "https://glygen.org/publication/PubMed/7997267", "database": "PubMed", "categories": [ "Other" ] }, { "id": "8816475", "url": "https://glygen.org/publication/PubMed/8816475", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q05397", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q05397*", "database": "IntAct", "categories": [ "Other" ] }, { "id": "7597091", "url": "https://glygen.org/publication/PubMed/7597091", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397", "database": "PRO", "categories": [ "Other" ] }, { "id": "10958798", "url": "https://glygen.org/publication/PubMed/10958798", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11606050", "url": "https://glygen.org/publication/PubMed/11606050", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12788385", "url": "https://glygen.org/publication/PubMed/12788385", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14604860", "url": "https://glygen.org/publication/PubMed/14604860", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14703945", "url": "https://glygen.org/publication/PubMed/14703945", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15817476", "url": "https://glygen.org/publication/PubMed/15817476", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17438336", "url": "https://glygen.org/publication/PubMed/17438336", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17478078", "url": "https://glygen.org/publication/PubMed/17478078", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18032789", "url": "https://glygen.org/publication/PubMed/18032789", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18182379", "url": "https://glygen.org/publication/PubMed/18182379", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18400991", "url": "https://glygen.org/publication/PubMed/18400991", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19826415", "url": "https://glygen.org/publication/PubMed/19826415", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19834610", "url": "https://glygen.org/publication/PubMed/19834610", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20124721", "url": "https://glygen.org/publication/PubMed/20124721", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20602165", "url": "https://glygen.org/publication/PubMed/20602165", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21359179", "url": "https://glygen.org/publication/PubMed/21359179", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22349353", "url": "https://glygen.org/publication/PubMed/22349353", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22356893", "url": "https://glygen.org/publication/PubMed/22356893", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22641287", "url": "https://glygen.org/publication/PubMed/22641287", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22710722", "url": "https://glygen.org/publication/PubMed/22710722", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23530035", "url": "https://glygen.org/publication/PubMed/23530035", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23817042", "url": "https://glygen.org/publication/PubMed/23817042", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23958855", "url": "https://glygen.org/publication/PubMed/23958855", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24025096", "url": "https://glygen.org/publication/PubMed/24025096", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24409152", "url": "https://glygen.org/publication/PubMed/24409152", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24586773", "url": "https://glygen.org/publication/PubMed/24586773", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24742605", "url": "https://glygen.org/publication/PubMed/24742605", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24999733", "url": "https://glygen.org/publication/PubMed/24999733", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25056351", "url": "https://glygen.org/publication/PubMed/25056351", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25337707", "url": "https://glygen.org/publication/PubMed/25337707", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25866790", "url": "https://glygen.org/publication/PubMed/25866790", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26456697", "url": "https://glygen.org/publication/PubMed/26456697", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26556867", "url": "https://glygen.org/publication/PubMed/26556867", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26689988", "url": "https://glygen.org/publication/PubMed/26689988", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27321183", "url": "https://glygen.org/publication/PubMed/27321183", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27344177", "url": "https://glygen.org/publication/PubMed/27344177", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27460083", "url": "https://glygen.org/publication/PubMed/27460083", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27462783", "url": "https://glygen.org/publication/PubMed/27462783", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27926483", "url": "https://glygen.org/publication/PubMed/27926483", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27956712", "url": "https://glygen.org/publication/PubMed/27956712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28076322", "url": "https://glygen.org/publication/PubMed/28076322", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28270217", "url": "https://glygen.org/publication/PubMed/28270217", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28624785", "url": "https://glygen.org/publication/PubMed/28624785", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28667800", "url": "https://glygen.org/publication/PubMed/28667800", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28755662", "url": "https://glygen.org/publication/PubMed/28755662", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28881794", "url": "https://glygen.org/publication/PubMed/28881794", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29069627", "url": "https://glygen.org/publication/PubMed/29069627", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29228301", "url": "https://glygen.org/publication/PubMed/29228301", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29292531", "url": "https://glygen.org/publication/PubMed/29292531", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29662665", "url": "https://glygen.org/publication/PubMed/29662665", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29748541", "url": "https://glygen.org/publication/PubMed/29748541", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29903032", "url": "https://glygen.org/publication/PubMed/29903032", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30262433", "url": "https://glygen.org/publication/PubMed/30262433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30285892", "url": "https://glygen.org/publication/PubMed/30285892", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30717801", "url": "https://glygen.org/publication/PubMed/30717801", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31215502", "url": "https://glygen.org/publication/PubMed/31215502", "database": "PubMed", "categories": [ "Other" ] }, { "id": "31501460", "url": "https://glygen.org/publication/PubMed/31501460", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32316668", "url": "https://glygen.org/publication/PubMed/32316668", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32337793", "url": "https://glygen.org/publication/PubMed/32337793", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32526166", "url": "https://glygen.org/publication/PubMed/32526166", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32751931", "url": "https://glygen.org/publication/PubMed/32751931", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33050159", "url": "https://glygen.org/publication/PubMed/33050159", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33420364", "url": "https://glygen.org/publication/PubMed/33420364", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634", "database": "PubMed", "categories": [ "Other" ] }, { "id": "33750427", "url": "https://glygen.org/publication/PubMed/33750427", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35569251", "url": "https://glygen.org/publication/PubMed/35569251", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35646067", "url": "https://glygen.org/publication/PubMed/35646067", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35682554", "url": "https://glygen.org/publication/PubMed/35682554", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35982848", "url": "https://glygen.org/publication/PubMed/35982848", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36001146", "url": "https://glygen.org/publication/PubMed/36001146", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9087451", "url": "https://glygen.org/publication/PubMed/9087451", "database": "PubMed", "categories": [ "Other" ] }, { "id": "9148935", "url": "https://glygen.org/publication/PubMed/9148935", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QPQEISPPPTANLDRSNDKV", "down_seq": "ENVTGLVKAVIEMSSKIQPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P07949-1", "kinase_gene_name": "RET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16153436", "url": "https://glygen.org/publication/PubMed/16153436" }, { "database": "PubMed", "id": "21454698", "url": "https://glygen.org/publication/PubMed/21454698" } ], "site_lbl": "Tyr925" }, { "kinase_uniprot_canonical_ac": "P08581-1", "kinase_gene_name": "MET", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "16782899", "url": "https://glygen.org/publication/PubMed/16782899" } ], "site_lbl": "Tyr925" }, { "kinase_uniprot_canonical_ac": "P09769-1", "kinase_gene_name": "FGR", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" } ], "site_lbl": "Tyr925" }, { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "7997267", "url": "https://glygen.org/publication/PubMed/7997267" }, { "database": "PubMed", "id": "8816475", "url": "https://glygen.org/publication/PubMed/8816475" } ], "site_lbl": "Tyr925" }, { "kinase_uniprot_canonical_ac": "P16591-1", "kinase_gene_name": "FER", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" } ], "site_lbl": "Tyr925" }, { "kinase_uniprot_canonical_ac": "Q05397-1", "kinase_gene_name": "PTK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "7997267", "url": "https://glygen.org/publication/PubMed/7997267" }, { "database": "PubMed", "id": "8816475", "url": "https://glygen.org/publication/PubMed/8816475" } ], "site_lbl": "Tyr925" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" }, { "database": "PubMed", "id": "12387730", "url": "https://glygen.org/publication/PubMed/12387730" }, { "database": "PubMed", "id": "19339212", "url": "https://glygen.org/publication/PubMed/19339212" }, { "database": "IntAct", "id": "Q05397", "url": "https://www.ebi.ac.uk/intact/interactors/id:Q05397*" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "7597091", "url": "https://glygen.org/publication/PubMed/7597091" }, { "database": "PRO", "id": "Q05397", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=Q05397" }, { "database": "PubMed", "id": "10958798", "url": "https://glygen.org/publication/PubMed/10958798" }, { "database": "PubMed", "id": "11606050", "url": "https://glygen.org/publication/PubMed/11606050" }, { "database": "PubMed", "id": "12788385", "url": "https://glygen.org/publication/PubMed/12788385" }, { "database": "PubMed", "id": "14604860", "url": "https://glygen.org/publication/PubMed/14604860" }, { "database": "PubMed", "id": "14703945", "url": "https://glygen.org/publication/PubMed/14703945" }, { "database": "PubMed", "id": "15263022", "url": "https://glygen.org/publication/PubMed/15263022" }, { "database": "PubMed", "id": "15735019", "url": "https://glygen.org/publication/PubMed/15735019" }, { "database": "PubMed", "id": "15817476", "url": "https://glygen.org/publication/PubMed/15817476" }, { "database": "PubMed", "id": "16275754", "url": "https://glygen.org/publication/PubMed/16275754" }, { "database": "PubMed", "id": "16917494", "url": "https://glygen.org/publication/PubMed/16917494" }, { "database": "PubMed", "id": "17117420", "url": "https://glygen.org/publication/PubMed/17117420" }, { "database": "PubMed", "id": "17219439", "url": "https://glygen.org/publication/PubMed/17219439" }, { "database": "PubMed", "id": "17438336", "url": "https://glygen.org/publication/PubMed/17438336" }, { "database": "PubMed", "id": "17478078", "url": "https://glygen.org/publication/PubMed/17478078" }, { "database": "PubMed", "id": "18032789", "url": "https://glygen.org/publication/PubMed/18032789" }, { "database": "PubMed", "id": "18182379", "url": "https://glygen.org/publication/PubMed/18182379" }, { "database": "PubMed", "id": "18343694", "url": "https://glygen.org/publication/PubMed/18343694" }, { "database": "PubMed", "id": "18349846", "url": "https://glygen.org/publication/PubMed/18349846" }, { "database": "PubMed", "id": "18400991", "url": "https://glygen.org/publication/PubMed/18400991" }, { "database": "PubMed", "id": "18805444", "url": "https://glygen.org/publication/PubMed/18805444" }, { "database": "PubMed", "id": "19190626", "url": "https://glygen.org/publication/PubMed/19190626" }, { "database": "PubMed", "id": "19568240", "url": "https://glygen.org/publication/PubMed/19568240" }, { "database": "PubMed", "id": "19657053", "url": "https://glygen.org/publication/PubMed/19657053" }, { "database": "PubMed", "id": "19740433", "url": "https://glygen.org/publication/PubMed/19740433" }, { "database": "PubMed", "id": "19826415", "url": "https://glygen.org/publication/PubMed/19826415" }, { "database": "PubMed", "id": "19834610", "url": "https://glygen.org/publication/PubMed/19834610" }, { "database": "PubMed", "id": "20124721", "url": "https://glygen.org/publication/PubMed/20124721" }, { "database": "PubMed", "id": "20378826", "url": "https://glygen.org/publication/PubMed/20378826" }, { "database": "PubMed", "id": "20602165", "url": "https://glygen.org/publication/PubMed/20602165" }, { "database": "PubMed", "id": "20955590", "url": "https://glygen.org/publication/PubMed/20955590" }, { "database": "PubMed", "id": "21084641", "url": "https://glygen.org/publication/PubMed/21084641" }, { "database": "PubMed", "id": "21359179", "url": "https://glygen.org/publication/PubMed/21359179" }, { "database": "PubMed", "id": "21716326", "url": "https://glygen.org/publication/PubMed/21716326" }, { "database": "PubMed", "id": "22349353", "url": "https://glygen.org/publication/PubMed/22349353" }, { "database": "PubMed", "id": "22356893", "url": "https://glygen.org/publication/PubMed/22356893" }, { "database": "PubMed", "id": "22641287", "url": "https://glygen.org/publication/PubMed/22641287" }, { "database": "PubMed", "id": "22710722", "url": "https://glygen.org/publication/PubMed/22710722" }, { "database": "PubMed", "id": "22824793", "url": "https://glygen.org/publication/PubMed/22824793" }, { "database": "PubMed", "id": "22938480", "url": "https://glygen.org/publication/PubMed/22938480" }, { "database": "PubMed", "id": "23209645", "url": "https://glygen.org/publication/PubMed/23209645" }, { "database": "PubMed", "id": "23530035", "url": "https://glygen.org/publication/PubMed/23530035" }, { "database": "PubMed", "id": "23817042", "url": "https://glygen.org/publication/PubMed/23817042" }, { "database": "PubMed", "id": "23933586", "url": "https://glygen.org/publication/PubMed/23933586" }, { "database": "PubMed", "id": "23958855", "url": "https://glygen.org/publication/PubMed/23958855" }, { "database": "PubMed", "id": "24025096", "url": "https://glygen.org/publication/PubMed/24025096" }, { "database": "PubMed", "id": "24409152", "url": "https://glygen.org/publication/PubMed/24409152" }, { "database": "PubMed", "id": "24586773", "url": "https://glygen.org/publication/PubMed/24586773" }, { "database": "PubMed", "id": "24642576", "url": "https://glygen.org/publication/PubMed/24642576" }, { "database": "PubMed", "id": "24681892", "url": "https://glygen.org/publication/PubMed/24681892" }, { "database": "PubMed", "id": "24736807", "url": "https://glygen.org/publication/PubMed/24736807" }, { "database": "PubMed", "id": "24742605", "url": "https://glygen.org/publication/PubMed/24742605" }, { "database": "PubMed", "id": "24885567", "url": "https://glygen.org/publication/PubMed/24885567" }, { "database": "PubMed", "id": "24999733", "url": "https://glygen.org/publication/PubMed/24999733" }, { "database": "PubMed", "id": "25056351", "url": "https://glygen.org/publication/PubMed/25056351" }, { "database": "PubMed", "id": "25193862", "url": "https://glygen.org/publication/PubMed/25193862" }, { "database": "PubMed", "id": "25337707", "url": "https://glygen.org/publication/PubMed/25337707" }, { "database": "PubMed", "id": "25611393", "url": "https://glygen.org/publication/PubMed/25611393" }, { "database": "PubMed", "id": "25778692", "url": "https://glygen.org/publication/PubMed/25778692" }, { "database": "PubMed", "id": "25866790", "url": "https://glygen.org/publication/PubMed/25866790" }, { "database": "PubMed", "id": "25949790", "url": "https://glygen.org/publication/PubMed/25949790" }, { "database": "PubMed", "id": "26456697", "url": "https://glygen.org/publication/PubMed/26456697" }, { "database": "PubMed", "id": "26556867", "url": "https://glygen.org/publication/PubMed/26556867" }, { "database": "PubMed", "id": "26689988", "url": "https://glygen.org/publication/PubMed/26689988" }, { "database": "PubMed", "id": "27145276", "url": "https://glygen.org/publication/PubMed/27145276" }, { "database": "PubMed", "id": "27286256", "url": "https://glygen.org/publication/PubMed/27286256" }, { "database": "PubMed", "id": "27321183", "url": "https://glygen.org/publication/PubMed/27321183" }, { "database": "PubMed", "id": "27344177", "url": "https://glygen.org/publication/PubMed/27344177" }, { "database": "PubMed", "id": "27460083", "url": "https://glygen.org/publication/PubMed/27460083" }, { "database": "PubMed", "id": "27462783", "url": "https://glygen.org/publication/PubMed/27462783" }, { "database": "PubMed", "id": "27926483", "url": "https://glygen.org/publication/PubMed/27926483" }, { "database": "PubMed", "id": "27956712", "url": "https://glygen.org/publication/PubMed/27956712" }, { "database": "PubMed", "id": "28076322", "url": "https://glygen.org/publication/PubMed/28076322" }, { "database": "PubMed", "id": "28270217", "url": "https://glygen.org/publication/PubMed/28270217" }, { "database": "PubMed", "id": "28624785", "url": "https://glygen.org/publication/PubMed/28624785" }, { "database": "PubMed", "id": "28667800", "url": "https://glygen.org/publication/PubMed/28667800" }, { "database": "PubMed", "id": "28755662", "url": "https://glygen.org/publication/PubMed/28755662" }, { "database": "PubMed", "id": "28881794", "url": "https://glygen.org/publication/PubMed/28881794" }, { "database": "PubMed", "id": "29050315", "url": "https://glygen.org/publication/PubMed/29050315" }, { "database": "PubMed", "id": "29069627", "url": "https://glygen.org/publication/PubMed/29069627" }, { "database": "PubMed", "id": "29228301", "url": "https://glygen.org/publication/PubMed/29228301" }, { "database": "PubMed", "id": "29292531", "url": "https://glygen.org/publication/PubMed/29292531" }, { "database": "PubMed", "id": "29662665", "url": "https://glygen.org/publication/PubMed/29662665" }, { "database": "PubMed", "id": "29748541", "url": "https://glygen.org/publication/PubMed/29748541" }, { "database": "PubMed", "id": "29903032", "url": "https://glygen.org/publication/PubMed/29903032" }, { "database": "PubMed", "id": "29928374", "url": "https://glygen.org/publication/PubMed/29928374" }, { "database": "PubMed", "id": "30262433", "url": "https://glygen.org/publication/PubMed/30262433" }, { "database": "PubMed", "id": "30285892", "url": "https://glygen.org/publication/PubMed/30285892" }, { "database": "PubMed", "id": "30347788", "url": "https://glygen.org/publication/PubMed/30347788" }, { "database": "PubMed", "id": "30498362", "url": "https://glygen.org/publication/PubMed/30498362" }, { "database": "PubMed", "id": "30717801", "url": "https://glygen.org/publication/PubMed/30717801" }, { "database": "PubMed", "id": "31215502", "url": "https://glygen.org/publication/PubMed/31215502" }, { "database": "PubMed", "id": "31501460", "url": "https://glygen.org/publication/PubMed/31501460" }, { "database": "PubMed", "id": "32274611", "url": "https://glygen.org/publication/PubMed/32274611" }, { "database": "PubMed", "id": "32316668", "url": "https://glygen.org/publication/PubMed/32316668" }, { "database": "PubMed", "id": "32337793", "url": "https://glygen.org/publication/PubMed/32337793" }, { "database": "PubMed", "id": "32526166", "url": "https://glygen.org/publication/PubMed/32526166" }, { "database": "PubMed", "id": "32751931", "url": "https://glygen.org/publication/PubMed/32751931" }, { "database": "PubMed", "id": "33050159", "url": "https://glygen.org/publication/PubMed/33050159" }, { "database": "PubMed", "id": "33420364", "url": "https://glygen.org/publication/PubMed/33420364" }, { "database": "PubMed", "id": "33614634", "url": "https://glygen.org/publication/PubMed/33614634" }, { "database": "PubMed", "id": "33750427", "url": "https://glygen.org/publication/PubMed/33750427" }, { "database": "PubMed", "id": "35569251", "url": "https://glygen.org/publication/PubMed/35569251" }, { "database": "PubMed", "id": "35646067", "url": "https://glygen.org/publication/PubMed/35646067" }, { "database": "PubMed", "id": "35682554", "url": "https://glygen.org/publication/PubMed/35682554" }, { "database": "PubMed", "id": "35982848", "url": "https://glygen.org/publication/PubMed/35982848" }, { "database": "PubMed", "id": "36001146", "url": "https://glygen.org/publication/PubMed/36001146" }, { "database": "PubMed", "id": "8816475", "url": "https://glygen.org/publication/PubMed/8816475" }, { "database": "PubMed", "id": "9087451", "url": "https://glygen.org/publication/PubMed/9087451" }, { "database": "PubMed", "id": "9148935", "url": "https://glygen.org/publication/PubMed/9148935" } ], "site_lbl": "Tyr925" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q05397-1.910.910", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q05397-1.914.914", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q05397-1.918.918", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q05397-1.923.923", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q05397-1.928.928", "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": 7 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 116 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q05397-1.963.963", "start_pos": 963, "end_pos": 963, "uniprot_canonical_ac": "Q05397-1", "length": 1052, "uniprot_id": "FAK1_HUMAN", "protein_name": "Focal adhesion kinase 1", "refseq_ac": "NP_001186578", "refseq_name": "focal adhesion kinase 1 isoform 3", "gene_name": "PTK2", "gene_names_uniprotkb": "PTK2; FAK1; FAK", "gene_names_refseq": "FADK 1; FADK; FAK1; FAK; FRNK; PPP1R71; PTK2; p125FAK; pp125FAK", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q05397", "url": "https://www.uniprot.org/uniprotkb/Q05397" } ], "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": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" } ], "reference": [ { "type": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" } ] } ], "crossref": [ { "id": "Q05397", "url": "https://www.iedb.org/epitope/Q05397", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QPAPPEEYVPMVKEVGLALR", "down_seq": "LLATVDETIPLLPASTHREI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q05397", "url": "https://www.iedb.org/epitope/Q05397" }, { "database": "iPTMnet", "id": "Q05397", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q05397" }, { "database": "PubMed", "id": "27869121", "url": "https://glygen.org/publication/PubMed/27869121" } ], "site_lbl": "Thr963" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "15", "end_pos": "15" }, { "start_pos": "458", "end_pos": "458" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1034", "end_pos": "1034" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "928", "end_pos": "928" } ] }, { "type": "snv", "site_list": [ { "start_pos": "127", "end_pos": "127" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "17", "end_pos": "17" }, { "start_pos": "255", "end_pos": "255" }, { "start_pos": "286", "end_pos": "286" }, { "start_pos": "290", "end_pos": "290" }, { "start_pos": "337", "end_pos": "337" }, { "start_pos": "341", "end_pos": "341" }, { "start_pos": "363", "end_pos": "363" }, { "start_pos": "385", "end_pos": "385" }, { "start_pos": "458", "end_pos": "458" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "634", "end_pos": "634" }, { "start_pos": "648", "end_pos": "648" }, { "start_pos": "767", "end_pos": "767" }, { "start_pos": "779", "end_pos": "779" }, { "start_pos": "790", "end_pos": "790" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "918", "end_pos": "918" }, { "start_pos": "923", "end_pos": "923" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1007", "end_pos": "1007" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "13", "end_pos": "13" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "390", "end_pos": "390" }, { "start_pos": "397", "end_pos": "397" }, { "start_pos": "407", "end_pos": "407" }, { "start_pos": "441", "end_pos": "441" }, { "start_pos": "474", "end_pos": "474" }, { "start_pos": "503", "end_pos": "503" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "568", "end_pos": "568" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "577", "end_pos": "577" }, { "start_pos": "580", "end_pos": "580" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "695", "end_pos": "695" }, { "start_pos": "700", "end_pos": "700" }, { "start_pos": "705", "end_pos": "705" }, { "start_pos": "716", "end_pos": "716" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "726", "end_pos": "726" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "742", "end_pos": "742" }, { "start_pos": "840", "end_pos": "840" }, { "start_pos": "843", "end_pos": "843" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "887", "end_pos": "887" }, { "start_pos": "892", "end_pos": "892" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "925", "end_pos": "925" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "P98194-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of a gain-of-function mutation in a Golgi P-type ATPase that enhances Mn2+ efflux and protects against toxicity.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Mukhopadhyay S, Linstedt AD", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "reference": [ { "type": "PubMed", "id": "21187401", "url": "https://glygen.org/publication/PubMed/21187401" } ] } ], "crossref": [ { "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21187401", "url": "https://glygen.org/publication/PubMed/21187401", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AIVKKLPIVETLGCCNVICS", "down_seq": "KTGTLTKNEMTVTHIFTSDG", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Impairs pump activity.", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" }, { "database": "PubMed", "id": "21187401", "url": "https://glygen.org/publication/PubMed/21187401" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "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": "P98194-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An N-terminal Ca(2+)-binding motif regulates the secretory pathway Ca(2+)/Mn(2+)-transport ATPase SPCA1.", "journal": "The Journal of biological chemistry", "date": "2019", "authors": "Chen J, Smaardijk S, Mattelaer CA, Pamula F, Vandecaetsbeek I, Vanoevelen J, Wuytack F, Lescrinier E, Eggermont J, Vangheluwe P", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "reference": [ { "type": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] } ], "crossref": [ { "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PVLTSKKASELPVSEVASIL", "down_seq": "ADLQNGLNKCEVSHRRAFHG", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "C", "comment": "Decreases calcium-dependent autophosphorylation.", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" }, { "database": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P98194-1.41.41", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P98194-1.50.50", "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": "P98194-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An N-terminal Ca(2+)-binding motif regulates the secretory pathway Ca(2+)/Mn(2+)-transport ATPase SPCA1.", "journal": "The Journal of biological chemistry", "date": "2019", "authors": "Chen J, Smaardijk S, Mattelaer CA, Pamula F, Vandecaetsbeek I, Vanoevelen J, Wuytack F, Lescrinier E, Eggermont J, Vangheluwe P", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "reference": [ { "type": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] } ], "crossref": [ { "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LTSKKASELPVSEVASILQA", "down_seq": "LQNGLNKCEVSHRRAFHGWN", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Decreases calcium-dependent autophosphorylation and the ATPase activity; when associated with A-50.", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" }, { "database": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P98194-1.39.39", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P98194-1.50.50", "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": "P98194-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An N-terminal Ca(2+)-binding motif regulates the secretory pathway Ca(2+)/Mn(2+)-transport ATPase SPCA1.", "journal": "The Journal of biological chemistry", "date": "2019", "authors": "Chen J, Smaardijk S, Mattelaer CA, Pamula F, Vandecaetsbeek I, Vanoevelen J, Wuytack F, Lescrinier E, Eggermont J, Vangheluwe P", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "reference": [ { "type": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] } ], "crossref": [ { "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PVSEVASILQADLQNGLNKC", "down_seq": "VSHRRAFHGWNEFDISEDEP", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Decreases calcium-dependent autophosphorylation and the ATPase activity; when associated with A-41.", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" }, { "database": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] }, { "sequence_org": "E", "sequence_mut": "S", "comment": "Decreases calcium-dependent autophosphorylation.", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" }, { "database": "PubMed", "id": "30923126", "url": "https://glygen.org/publication/PubMed/30923126" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "P98194-1.39.39", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P98194-1.41.41", "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": "P98194-1.747.747", "start_pos": 747, "end_pos": 747, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Identification of a gain-of-function mutation in a Golgi P-type ATPase that enhances Mn2+ efflux and protects against toxicity.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Mukhopadhyay S, Linstedt AD", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "reference": [ { "type": "PubMed", "id": "21187401", "url": "https://glygen.org/publication/PubMed/21187401" } ] } ], "crossref": [ { "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21187401", "url": "https://glygen.org/publication/PubMed/21187401", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "NPLNAMQILWINIIMDGPPA", "down_seq": "SLGVEPVDKDVIRKPPRNWK", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Increases manganese transporter activity.", "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" }, { "database": "PubMed", "id": "21187401", "url": "https://glygen.org/publication/PubMed/21187401" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "P98194-1.764.764", "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": "P98194-1.422.422", "start_pos": 422, "end_pos": 422, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P98194", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "SRIVEAGCVCNDAVIRNNTL", "down_seq": "GKPTEGALIALAMKMGLDGL", "snv": [ { "evidence": [ { "id": "P98194", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194" } ], "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": "3", "chr_pos": "130967377", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M422", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID: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": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P98194-1.420.420", "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": "P98194-1.690.690", "start_pos": 690, "end_pos": 690, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P98194", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KEAADMILVDDDFQTIMSAI", "down_seq": "EGKGIYNNIKNFVRFQLSTS", "snv": [ { "evidence": [ { "id": "P98194", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194" } ], "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": "3", "chr_pos": "130996053", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E690", "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: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": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "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": "P98194-1.764.764", "start_pos": 764, "end_pos": 764, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P98194", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PPAQSLGVEPVDKDVIRKPP", "down_seq": "NWKDSILTKNLILKILVSSI", "snv": [ { "evidence": [ { "id": "P98194", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194" } ], "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 (5).", "chr_id": "3", "chr_pos": "130997653", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R764", "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: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": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P98194-1.747.747", "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": "P98194-1.806.806", "start_pos": 806, "end_pos": 806, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P98194", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "IVCGTLFVFWRELRDNVITP", "down_seq": "DTTMTFTCFVFFDMFNALSS", "snv": [ { "evidence": [ { "id": "P98194", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "130998319", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R806", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "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": "P98194-1.910.910", "start_pos": 910, "end_pos": 910, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P98194", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IVAEIIKKVERSREKIQKHV", "down_seq": "STSSSFLEV", "snv": [ { "evidence": [ { "id": "P98194", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P98194" } ], "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": "3", "chr_pos": "131001318", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S910", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P98194-1.911.911", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P98194-1.914.914", "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": "P98194-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "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": "P98194-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P98194", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194", "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": "AVSRIVEAGCVCNDAVIRNN", "down_seq": "LMGKPTEGALIALAMKMGLD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P98194", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr420" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P98194-1.422.422", "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": "P98194-1.911.911", "start_pos": 911, "end_pos": 911, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "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": "P98194-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P98194", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194", "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": "VAEIIKKVERSREKIQKHVS", "down_seq": "TSSSFLEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P98194", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser911" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P98194-1.910.910", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P98194-1.914.914", "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": "P98194-1.914.914", "start_pos": 914, "end_pos": 914, "uniprot_canonical_ac": "P98194-1", "length": 919, "uniprot_id": "AT2C1_HUMAN", "protein_name": "Calcium-transporting ATPase type 2C member 1", "refseq_ac": "NP_001001485", "refseq_name": "calcium-transporting ATPase type 2C member 1 isoform 1c", "gene_name": "ATP2C1", "gene_names_uniprotkb": "ATP2C1; HUSSY-28; KIAA1347; PMR1L", "gene_names_refseq": "ATP2C1A; ATP2C1; BCPM; HHD; PMR1; SPCA1; hSPCA1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P98194", "url": "https://www.uniprot.org/uniprotkb/P98194" } ], "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": "P98194-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194-1" } ], "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": "P98194-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P98194", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194", "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": "IIKKVERSREKIQKHVSSTS", "down_seq": "SFLEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P98194", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P98194" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser914" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "747", "end_pos": "747" } ] }, { "type": "snv", "site_list": [ { "start_pos": "422", "end_pos": "422" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "806", "end_pos": "806" }, { "start_pos": "910", "end_pos": "910" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "420", "end_pos": "420" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P98194-1.910.910", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P98194-1.911.911", "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": "Q15131-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "FBXO31-mediated ubiquitination of OGT maintains O-GlcNAcylation homeostasis to restrain endometrial malignancy.", "journal": "Nature communications", "date": "2025-02-02", "authors": "Zhang Na, Meng Yang, Mao Song, Ni Huiling, Huang Canhua, Shen Licong, Fu Kun, Lv Lu, Yu Chunhong, Meekrathok Piyanat, Kuang Chunmei, Chen Fang, Zhang Yu, Yuan Kai", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q15131", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15131" } ], "reference": [ { "type": "PubMed", "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887" } ] } ], "crossref": [ { "id": "39894887", "url": "https://glygen.org/publication/PubMed/39894887", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q15131", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15131", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "39894887", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39894887" }, { "id": "Q15131", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q15131" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "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": "Q15131-1.313.313", "start_pos": 313, "end_pos": 313, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15131", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SEAGLRLLHFLFMYDPKKRA", "down_seq": "AGDCLESSYFKEKPLPCEPE", "snv": [ { "evidence": [ { "id": "Q15131", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131" } ], "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: num. of cancers (3).", "chr_id": "16", "chr_pos": "89695298", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T313", "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: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: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": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "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": "Q15131-1.34.34", "start_pos": 34, "end_pos": 34, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15131", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KCIRKEGFFTVPPEHRLGRC", "down_seq": "SVKEFEKLNRIGEGTYGIVY", "snv": [ { "evidence": [ { "id": "Q15131", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131" } ], "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 (3).", "chr_id": "16", "chr_pos": "89689265", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R34", "disease": [ { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q15131-1.23.23", "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": "Q15131-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15131", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GEGTYGIVYRARDTQTDEIV", "down_seq": "LKKVRMDKEKDGIPISSLRE", "snv": [ { "evidence": [ { "id": "Q15131", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131" } ], "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": "16", "chr_pos": "89690588", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A66", "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": "snv", "site_list": [ { "start_pos": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "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": "Q15131-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q15131", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MDKEKDGIPISSLREITLLL", "down_seq": "LRHPNIVELKEVVVGNHLES", "snv": [ { "evidence": [ { "id": "Q15131", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q15131" } ], "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 (4).", "chr_id": "16", "chr_pos": "89691485", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R92", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID: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": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "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": "Q15131-1.196.196", "start_pos": 196, "end_pos": 196, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "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": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" }, { "database": "iPTMnet", "id": "Q15131-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131-1" } ], "reference": [ { "type": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" } ] }, { "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": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" }, { "database": "iPTMnet", "id": "Q15131-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131-1" } ], "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": "Q15131-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q15131", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131", "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": "CVKTADFGLARAYGVPVKPM", "down_seq": "PKVVTLWYRAPELLLGTTTQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" }, { "database": "PubMed", "id": "18691976", "url": "https://glygen.org/publication/PubMed/18691976" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q15131", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr196" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "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": "Q15131-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "Q15131-1", "length": 360, "uniprot_id": "CDK10_HUMAN", "protein_name": "Cyclin-dependent kinase 10", "refseq_ac": "NP_001092003", "refseq_name": "cyclin-dependent kinase 10 isoform c", "gene_name": "CDK10", "gene_names_uniprotkb": "CDK10", "gene_names_refseq": "ALSAS; CDK10; PISSLRE", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q15131", "url": "https://www.uniprot.org/uniprotkb/Q15131" } ], "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": "Q15131", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "Q15131", "url": "https://www.iedb.org/epitope/Q15131", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q15131", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131", "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": "EPDLECEQIRLKCIRKEGFF", "down_seq": "VPPEHRLGRCRSVKEFEKLN", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q15131", "url": "https://www.iedb.org/epitope/Q15131" }, { "database": "iPTMnet", "id": "Q15131", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q15131" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Thr23" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "313", "end_pos": "313" }, { "start_pos": "34", "end_pos": "34" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "92", "end_pos": "92" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "196", "end_pos": "196" }, { "start_pos": "23", "end_pos": "23" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q15131-1.34.34", "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": "Q12816-1.724.724", "start_pos": 724, "end_pos": 724, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "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": "Q12816", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "Q12816", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "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": "Q12816", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q12816", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q12816", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q12816", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs756443610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756443610", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756443610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756443610", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756443610", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756443610#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756443610", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756443610", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SFEIEARAQENADASTNVNF", "down_seq": "RGASTRAGFSDGASISFNGA", "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": "Ser724", "evidence": [ { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q12816", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q12816" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "snv": [ { "evidence": [ { "id": "rs756443610", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756443610" }, { "id": "rs756443610", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756443610" }, { "id": "rs756443610", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756443610#frequency_tab" }, { "id": "rs756443610", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756443610" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->G).", "chr_id": "X", "chr_pos": "54928894", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S724", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q12816-1.722.722", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q12816-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932256960", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932256960", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932256960", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1932256960", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TKAAPAAPPVPAANEIATNK", "down_seq": "KITWQALNLPVITQISQALP", "snv": [ { "evidence": [ { "id": "rs1932256960", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932256960" }, { "id": "rs1932256960", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1932256960" } ], "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": "X", "chr_pos": "54922830", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P100", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q12816-1.101.101", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1016.1016", "start_pos": 1016, "end_pos": 1016, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932946995", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932946995", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932946995", "url": "https://www.ensembl.org/id/rs1932946995", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SADFGGTLSTSVCFGGSPGT", "down_seq": "VSFGSALNTNAGYGGAVSTN", "snv": [ { "evidence": [ { "id": "rs1932946995", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932946995" }, { "id": "rs1932946995", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1932946995" } ], "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": "X", "chr_pos": "54929771", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1016", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q12816-1.1026.1026", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs759961860", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759961860", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs759961860", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759961860", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs759961860", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759961860#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs759961860", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759961860", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KAAPAAPPVPAANEIATNKP", "down_seq": "ITWQALNLPVITQISQALPT", "snv": [ { "evidence": [ { "id": "rs759961860", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759961860" }, { "id": "rs759961860", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs759961860" }, { "id": "rs759961860", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs759961860#frequency_tab" }, { "id": "rs759961860", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs759961860" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KIT->NIT).", "chr_id": "X", "chr_pos": "54922835", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K101", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q12816-1.100.100", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1026.1026", "start_pos": 1026, "end_pos": 1026, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750138156", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750138156", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750138156", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750138156", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750138156", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750138156", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750138156", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750138156", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SVCFGGSPGTSVSFGSALNT", "down_seq": "AGYGGAVSTNTDFGGTLSTS", "snv": [ { "evidence": [ { "id": "rs750138156", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750138156" }, { "id": "rs750138156", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750138156" }, { "id": "rs750138156", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750138156" }, { "id": "rs750138156", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750138156" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "X", "chr_pos": "54929801", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1026", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q12816-1.1016.1016", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1054.1054", "start_pos": 1054, "end_pos": 1054, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1419727444", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419727444", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1419727444", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419727444#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STNTDFGGTLSTSVCFGGSP", "down_seq": "TSAGFGGALNTNASFGCAVS", "snv": [ { "evidence": [ { "id": "rs1419727444", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1419727444" }, { "id": "rs1419727444", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1419727444#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 (STS->NTS).", "chr_id": "X", "chr_pos": "54929885", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1054", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q12816-1.1066.1066", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q12816-1.1073.1073", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q12816-1.1074.1074", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1066.1066", "start_pos": 1066, "end_pos": 1066, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764168100", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764168100", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764168100", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764168100", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs764168100", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764168100", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764168100", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764168100", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SVCFGGSPSTSAGFGGALNT", "down_seq": "ASFGCAVSTSASFSGAVSTS", "snv": [ { "evidence": [ { "id": "rs764168100", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764168100" }, { "id": "rs764168100", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764168100" }, { "id": "rs764168100", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764168100" }, { "id": "rs764168100", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764168100" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTN->NTS).", "chr_id": "X", "chr_pos": "54929921", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.0003", "site_lbl": "N1066", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q12816-1.1054.1054", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q12816-1.1073.1073", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q12816-1.1074.1074", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q12816-1.1076.1076", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q12816-1.1086.1086", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1073.1073", "start_pos": 1073, "end_pos": 1073, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PSTSAGFGGALNTNASFGCA", "down_seq": "STSASFSGAVSTSACFSGAP", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54929941", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V1073", "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: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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q12816-1.1054.1054", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q12816-1.1066.1066", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q12816-1.1074.1074", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q12816-1.1076.1076", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q12816-1.1086.1086", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1074.1074", "start_pos": 1074, "end_pos": 1074, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1219586716", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1219586716", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1219586716", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1219586716", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSAGFGGALNTNASFGCAV", "down_seq": "TSASFSGAVSTSACFSGAPI", "snv": [ { "evidence": [ { "id": "rs1219586716", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1219586716" }, { "id": "rs1219586716", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1219586716" } ], "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": "X", "chr_pos": "54929945", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1074", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q12816-1.1054.1054", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q12816-1.1066.1066", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q12816-1.1073.1073", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q12816-1.1076.1076", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q12816-1.1086.1086", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1076.1076", "start_pos": 1076, "end_pos": 1076, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SAGFGGALNTNASFGCAVST", "down_seq": "ASFSGAVSTSACFSGAPITN", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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 (SAS->NAS).", "chr_id": "23", "chr_pos": "54929951", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1076", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q12816-1.1066.1066", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q12816-1.1073.1073", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q12816-1.1074.1074", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q12816-1.1086.1086", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1086.1086", "start_pos": 1086, "end_pos": 1086, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932976818", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932976818", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932976818", "url": "https://www.ensembl.org/id/rs1932976818", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NASFGCAVSTSASFSGAVST", "down_seq": "ACFSGAPITNPGFGGAFSTS", "snv": [ { "evidence": [ { "id": "rs1932976818", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932976818" }, { "id": "rs1932976818", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1932976818" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SAC->NAC).", "chr_id": "X", "chr_pos": "54929981", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1086", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q12816-1.1066.1066", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q12816-1.1073.1073", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q12816-1.1074.1074", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q12816-1.1076.1076", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1124.1124", "start_pos": 1124, "end_pos": 1124, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1768265884", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1768265884", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1768265884", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1768265884#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSAGFGGALSTAADFGGTP", "down_seq": "NSIGFGAAPSTSVSFGGAHG", "snv": [ { "evidence": [ { "id": "rs1768265884", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1768265884" }, { "id": "rs1768265884", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1768265884#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 (SNS->NNS).", "chr_id": "X", "chr_pos": "54930095", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1124", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q12816-1.1127.1127", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q12816-1.1136.1136", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q12816-1.1143.1143", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1127.1127", "start_pos": 1127, "end_pos": 1127, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758795759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758795759", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758795759", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758795759", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758795759", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758795759", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AGFGGALSTAADFGGTPSNS", "down_seq": "GFGAAPSTSVSFGGAHGTSL", "snv": [ { "evidence": [ { "id": "rs758795759", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758795759" }, { "id": "rs758795759", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758795759" }, { "id": "rs758795759", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758795759" } ], "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": "X", "chr_pos": "54930104", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1127", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q12816-1.1124.1124", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q12816-1.1136.1136", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q12816-1.1143.1143", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1136.1136", "start_pos": 1136, "end_pos": 1136, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200531038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200531038", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200531038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200531038", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200531038", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200531038#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200531038", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200531038", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AADFGGTPSNSIGFGAAPST", "down_seq": "VSFGGAHGTSLCFGGAPSTS", "snv": [ { "evidence": [ { "id": "rs200531038", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200531038" }, { "id": "rs200531038", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200531038" }, { "id": "rs200531038", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200531038#frequency_tab" }, { "id": "rs200531038", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200531038" } ], "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": "X", "chr_pos": "54930131", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1136", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q12816-1.1124.1124", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q12816-1.1127.1127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q12816-1.1143.1143", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1143.1143", "start_pos": 1143, "end_pos": 1143, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs773310346", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773310346", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773310346", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773310346", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "PSNSIGFGAAPSTSVSFGGA", "down_seq": "GTSLCFGGAPSTSLCFGSAS", "snv": [ { "evidence": [ { "id": "rs773310346", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773310346" }, { "id": "rs773310346", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773310346" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HGT->NGT).", "chr_id": "X", "chr_pos": "54930151", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H1143", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q12816-1.1124.1124", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q12816-1.1127.1127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q12816-1.1136.1136", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.1174.1174", "start_pos": 1174, "end_pos": 1174, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSLCFGSASNTNLCFGGPP", "down_seq": "TSACFSGATSPSFCDGPSTS", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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 (STS->NTS).", "chr_id": "23", "chr_pos": "54930245", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1174", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.1234.1234", "start_pos": 1234, "end_pos": 1234, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs10284089", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs10284089", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs10284089", "url": "https://www.ncbi.nlm.nih.gov/snp/rs10284089#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NTSAGFGGGLGTSAGFSGGL", "down_seq": "TSSGFDGGLGTSAGFGGGPG", "snv": [ { "evidence": [ { "id": "rs10284089", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs10284089" }, { "id": "rs10284089", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs10284089#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 (STS->NTS).", "chr_id": "X", "chr_pos": "54930425", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1234", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.1317.1317", "start_pos": 1317, "end_pos": 1317, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ASFGSTLGTSAGFSGGLSTS", "down_seq": "GFGSRPNASFDRGLSTIIGF", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54930673", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D1317", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.1339.1339", "start_pos": 1339, "end_pos": 1339, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1369855115", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369855115", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1369855115", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369855115", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FGSRPNASFDRGLSTIIGFG", "down_seq": "GSNTSTGFTGEPSTSTGFSS", "snv": [ { "evidence": [ { "id": "rs1369855115", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1369855115" }, { "id": "rs1369855115", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1369855115" } ], "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": "X", "chr_pos": "54930740", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1339", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.1388.1388", "start_pos": 1388, "end_pos": 1388, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SGGPSTGVGFCSGPSTSGFS", "down_seq": "GPSTGAGFGGGPNTGAGFGG", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54930886", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1388", "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": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1488595239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488595239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1488595239", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1488595239", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "TEVTNTQASSVTAQPKKANK", "down_seq": "KRVTAKAAQGSQSPTGHEGG", "snv": [ { "evidence": [ { "id": "rs1488595239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488595239" }, { "id": "rs1488595239", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1488595239" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKM->NKT).", "chr_id": "X", "chr_pos": "54922957", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M142", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ALITSIKPKKASKAKKAANK", "down_seq": "IASATEVSLAATATHTATTQ", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NKA->NKS).", "chr_id": "23", "chr_pos": "54923175", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A215", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q12816-1.229.229", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.229.229", "start_pos": 229, "end_pos": 229, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776843249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776843249", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776843249", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776843249", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776843249", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776843249#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776843249", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776843249", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KKAANKAIASATEVSLAATA", "down_seq": "HTATTQGQITNETASIHTTA", "snv": [ { "evidence": [ { "id": "rs776843249", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776843249" }, { "id": "rs776843249", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776843249" }, { "id": "rs776843249", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776843249#frequency_tab" }, { "id": "rs776843249", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776843249" } ], "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 (THT->NHT).", "chr_id": "X", "chr_pos": "54923218", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T229", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q12816-1.215.215", "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": "Q12816-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TTQGQITNETASIHTTAASI", "down_seq": "TKKASKARKTIAKVINTDTE", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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": "23", "chr_pos": "54923290", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R253", "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: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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LADDYLAQLSLEPTTRTRGK", "down_seq": "NRKSKHLNGDERSGSNYRRI", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54923758", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R409", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.439.439", "start_pos": 439, "end_pos": 439, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DERSGSNYRRIPWGRRPAPP", "down_seq": "DVAILQERANKLVKYLLVKD", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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": "54924529", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R439", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q12816-1.459.459", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.459.459", "start_pos": 459, "end_pos": 459, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1464228593", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464228593", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1464228593", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1464228593", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1464228593", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1464228593", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RDVAILQERANKLVKYLLVK", "down_seq": "QTKIPIKRSDMLRDVIQEYD", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" }, { "id": "rs1464228593", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1464228593" }, { "id": "rs1464228593", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1464228593" }, { "id": "rs1464228593", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1464228593" } ], "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 (DQT->NQT).", "chr_id": "23", "chr_pos": "54924703", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D459", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q12816-1.439.439", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "SSLYILISTQESSAGILGTT", "down_seq": "DTPKLGLLMVILSVIFMNGN", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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 (KDT->NDT).", "chr_id": "23", "chr_pos": "54926416", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K528", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.560.560", "start_pos": 560, "end_pos": 560, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LSVIFMNGNKASEAVIWEVL", "down_seq": "KLGLRPGVRHSLFGEVRKLI", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54926604", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R560", "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: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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q12816-1.565.565", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.565.565", "start_pos": 565, "end_pos": 565, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MNGNKASEAVIWEVLRKLGL", "down_seq": "PGVRHSLFGEVRKLITDEFV", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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": "23", "chr_pos": "54926619", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R565", "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" } ] }, { "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q12816-1.560.560", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.610.610", "start_pos": 610, "end_pos": 610, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LEYKRVPNSRPPEYEFFWGL", "down_seq": "SYHETSKMKVLKFACRVQKK", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54927731", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R610", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.686.686", "start_pos": 686, "end_pos": 686, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QMGIGEEAVAGPWNWDDMDI", "down_seq": "CLTREELGDDAQAWSRFSFE", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "54928780", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D686", "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: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: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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1280874524", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1280874524", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1280874524", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1280874524", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LAATKDSLAMDPPVVNRPKK", "down_seq": "KTKKAPIKTITKAAPAAPPV", "snv": [ { "evidence": [ { "id": "rs1280874524", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1280874524" }, { "id": "rs1280874524", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1280874524" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKT->NKT).", "chr_id": "X", "chr_pos": "54922738", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S69", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "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": "Q12816-1.722.722", "start_pos": 722, "end_pos": 722, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764109033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764109033", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764109033", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764109033", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs764109033", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764109033", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764109033", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764109033#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs764109033", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764109033", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RFSFEIEARAQENADASTNV", "down_seq": "FSRGASTRAGFSDGASISFN", "snv": [ { "evidence": [ { "id": "rs764109033", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764109033" }, { "id": "rs764109033", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs764109033" }, { "id": "rs764109033", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764109033" }, { "id": "rs764109033", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs764109033#frequency_tab" }, { "id": "rs764109033", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764109033" } ], "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 (NVN->NVS).", "chr_id": "X", "chr_pos": "54928889", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N722", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q12816-1.724.724", "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": "Q12816-1.764.764", "start_pos": 764, "end_pos": 764, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APSSSGGFSGGPGITFGVAP", "down_seq": "TSASFSNTASISFGGTLSTS", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "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 (STS->NTS).", "chr_id": "23", "chr_pos": "54929015", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S764", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q12816-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q12816-1.773.773", "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": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.770.770", "start_pos": 770, "end_pos": 770, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932882067", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932882067", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932882067", "url": "https://www.ensembl.org/id/rs1932882067", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GFSGGPGITFGVAPSTSASF", "down_seq": "NTASISFGGTLSTSSSFSSA", "snv": [ { "evidence": [ { "id": "rs1932882067", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932882067" }, { "id": "rs1932882067", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1932882067" } ], "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": "X", "chr_pos": "54929033", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S770", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q12816-1.764.764", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q12816-1.773.773", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.773.773", "start_pos": 773, "end_pos": 773, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1396397888", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1396397888", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1396397888", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1396397888#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GGPGITFGVAPSTSASFSNT", "down_seq": "SISFGGTLSTSSSFSSAASI", "snv": [ { "evidence": [ { "id": "rs1396397888", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1396397888" }, { "id": "rs1396397888", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1396397888#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "X", "chr_pos": "54929041", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A773", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q12816-1.764.764", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q12816-1.770.770", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q12816-1.792.792", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.792.792", "start_pos": 792, "end_pos": 792, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932889536", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932889536", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932889536", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1932889536", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TASISFGGTLSTSSSFSSAA", "down_seq": "ISFGCAHSTSTSFSSEASIS", "snv": [ { "evidence": [ { "id": "rs1932889536", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932889536" }, { "id": "rs1932889536", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1932889536" } ], "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 (SIS->NIS).", "chr_id": "X", "chr_pos": "54929099", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S792", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q12816-1.773.773", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q12816-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q12816-1.810.810", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.800.800", "start_pos": 800, "end_pos": 800, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1309197634", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309197634", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1309197634", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309197634", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TLSTSSSFSSAASISFGCAH", "down_seq": "TSTSFSSEASISFGGMPCTS", "snv": [ { "evidence": [ { "id": "rs1309197634", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1309197634" }, { "id": "rs1309197634", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1309197634" } ], "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": "X", "chr_pos": "54929123", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S800", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q12816-1.792.792", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q12816-1.810.810", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q12816-1.820.820", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.810.810", "start_pos": 810, "end_pos": 810, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932892919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932892919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932892919", "url": "https://www.ensembl.org/id/rs1932892919", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AASISFGCAHSTSTSFSSEA", "down_seq": "ISFGGMPCTSASFSGGVSSS", "snv": [ { "evidence": [ { "id": "rs1932892919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932892919" }, { "id": "rs1932892919", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1932892919" } ], "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 (SIS->NIS).", "chr_id": "X", "chr_pos": "54929153", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S810", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q12816-1.792.792", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q12816-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q12816-1.820.820", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q12816-1.822.822", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.820.820", "start_pos": 820, "end_pos": 820, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSTSFSSEASISFGGMPCT", "down_seq": "ASFSGGVSSSFSGPLSTSAT", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SAS->NAS).", "chr_id": "23", "chr_pos": "54929183", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S820", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q12816-1.800.800", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q12816-1.810.810", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q12816-1.822.822", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q12816-1.836.836", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.822.822", "start_pos": 822, "end_pos": 822, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs770372598", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770372598", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770372598", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770372598", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770372598", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770372598#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770372598", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770372598", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs770372598", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770372598", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSFSSEASISFGGMPCTSA", "down_seq": "FSGGVSSSFSGPLSTSATFS", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" }, { "id": "rs770372598", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770372598" }, { "id": "rs770372598", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770372598" }, { "id": "rs770372598", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770372598#frequency_tab" }, { "id": "rs770372598", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770372598" }, { "id": "rs770372598", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770372598" } ], "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": "23", "chr_pos": "54929189", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S822", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q12816-1.810.810", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q12816-1.820.820", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q12816-1.836.836", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.836.836", "start_pos": 836, "end_pos": 836, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MPCTSASFSGGVSSSFSGPL", "down_seq": "TSATFSGGASSGFGGTLSTT", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (STS->NTS).", "chr_id": "23", "chr_pos": "54929231", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S836", "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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q12816-1.820.820", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q12816-1.822.822", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.875.875", "start_pos": 875, "end_pos": 875, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TTAGFSGVLSTSTSFGSAPT", "down_seq": "STVFSSALSTSTGFGGILST", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "54929348", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T875", "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: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": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q12816-1.894.894", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.894.894", "start_pos": 894, "end_pos": 894, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1932912917", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932912917", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1932912917", "url": "https://www.ensembl.org/id/rs1932912917", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTSTVFSSALSTSTGFGGIL", "down_seq": "TSVCFGGSPSSSGSFGGTLS", "snv": [ { "evidence": [ { "id": "rs1932912917", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1932912917" }, { "id": "rs1932912917", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1932912917" } ], "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": "X", "chr_pos": "54929405", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S894", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q12816-1.875.875", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q12816-1.904.904", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.904.904", "start_pos": 904, "end_pos": 904, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q12816", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STSTGFGGILSTSVCFGGSP", "down_seq": "SSGSFGGTLSTSICFGGSPC", "snv": [ { "evidence": [ { "id": "Q12816", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q12816" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (SSS->NSS).", "chr_id": "23", "chr_pos": "54929435", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S904", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q12816-1.894.894", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.944.944", "start_pos": 944, "end_pos": 944, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200016772", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200016772", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200016772", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200016772", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "CTSTGFGGTLSTSVSFGGSS", "down_seq": "TSANFGGTLSTSICFDGSPS", "snv": [ { "evidence": [ { "id": "rs200016772", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200016772" }, { "id": "rs200016772", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200016772" } ], "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": "X", "chr_pos": "54929555", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S944", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q12816-1.960.960", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.960.960", "start_pos": 960, "end_pos": 960, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1260860393", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260860393", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1260860393", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260860393", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GGSSSTSANFGGTLSTSICF", "down_seq": "GSPSTGAGFGGALNTSASFG", "snv": [ { "evidence": [ { "id": "rs1260860393", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260860393" }, { "id": "rs1260860393", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260860393" } ], "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": "X", "chr_pos": "54929602", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D960", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q12816-1.944.944", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q12816-1.976.976", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q12816-1.976.976", "start_pos": 976, "end_pos": 976, "uniprot_canonical_ac": "Q12816-1", "length": 1431, "uniprot_id": "TROP_HUMAN", "protein_name": "Trophinin", "refseq_ac": "NP_001034794", "refseq_name": "trophinin isoform 5", "gene_name": "TRO", "gene_names_uniprotkb": "TRO; KIAA1114; MAGED3", "gene_names_refseq": "MAGE-d3; MAGED3; TRO", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q12816", "url": "https://www.uniprot.org/uniprotkb/Q12816" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1173203674", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173203674", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1173203674", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173203674", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SICFDGSPSTGAGFGGALNT", "down_seq": "ASFGSVLNTSTGFGGAMSTS", "snv": [ { "evidence": [ { "id": "rs1173203674", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1173203674" }, { "id": "rs1173203674", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1173203674" } ], "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 (SAS->NAS).", "chr_id": "X", "chr_pos": "54929651", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S976", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "724", "end_pos": "724" } ] }, { "type": "snv", "site_list": [ { "start_pos": "100", "end_pos": "100" }, { "start_pos": "1016", "end_pos": "1016" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "1026", "end_pos": "1026" }, { "start_pos": "1054", "end_pos": "1054" }, { "start_pos": "1066", "end_pos": "1066" }, { "start_pos": "1073", "end_pos": "1073" }, { "start_pos": "1074", "end_pos": "1074" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1086", "end_pos": "1086" }, { "start_pos": "1124", "end_pos": "1124" }, { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1143", "end_pos": "1143" }, { "start_pos": "1174", "end_pos": "1174" }, { "start_pos": "1234", "end_pos": "1234" }, { "start_pos": "1317", "end_pos": "1317" }, { "start_pos": "1339", "end_pos": "1339" }, { "start_pos": "1388", "end_pos": "1388" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "215", "end_pos": "215" }, { "start_pos": "229", "end_pos": "229" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "439", "end_pos": "439" }, { "start_pos": "459", "end_pos": "459" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "686", "end_pos": "686" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "722", "end_pos": "722" }, { "start_pos": "724", "end_pos": "724" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "770", "end_pos": "770" }, { "start_pos": "773", "end_pos": "773" }, { "start_pos": "792", "end_pos": "792" }, { "start_pos": "800", "end_pos": "800" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "822", "end_pos": "822" }, { "start_pos": "836", "end_pos": "836" }, { "start_pos": "875", "end_pos": "875" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "904", "end_pos": "904" }, { "start_pos": "944", "end_pos": "944" }, { "start_pos": "960", "end_pos": "960" }, { "start_pos": "976", "end_pos": "976" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q12816-1.960.960", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.1069.1069", "start_pos": 1069, "end_pos": 1069, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "CTSKIGQTNARGKDLDTDFT", "down_seq": "NASQPETKAIIENLIQKQDF", "glycosylation": [ { "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": "Asn1069", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O75976-1.1059.1059", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.1071.1071", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.1072.1072", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.1070.1070", "start_pos": 1070, "end_pos": 1070, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TSKIGQTNARGKDLDTDFTN", "down_seq": "ASQPETKAIIENLIQKQDFS", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G02886BB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G07755XJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G10773YW", "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G18647XP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G20210JR", "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G23984SE", "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G25079LO", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G25451PN", "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G60033FS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G65184UU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G70619PT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G72747WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "GKDLDTDFTNNASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G83229XP", "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G85269DF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G92062TF", "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": "Asn1070", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G95177YH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "G98611JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DLDTDFTNnASQPETK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1070", "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": "Asn1070", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75976-1.1059.1059", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.1069.1069", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.1071.1071", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.1072.1072", "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": 39 }, { "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": 38 }, { "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": 38 } ], "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": 38 }, { "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": 38 }, { "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": 38 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.1142.1142", "start_pos": 1142, "end_pos": 1142, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "rs777580072", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777580072", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777580072", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777580072", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777580072", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777580072", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1913293262", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913293262", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1913293262", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1913293262", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1913293262", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1913293262", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LASLYANNHPSMHMGQPSCP", "down_seq": "KSDENIPGGVMRGAEWHSHL", "glycosylation": [ { "glytoucan_ac": "G29015LH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HLASLYANNHPSMHMGQPSCPNK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1142", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn1142", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "rs777580072", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777580072" }, { "id": "rs777580072", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777580072" }, { "id": "rs777580072", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777580072" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NKS->DKS).", "chr_id": "17", "chr_pos": "30456342", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1142", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKS->HKS).", "chr_id": "17", "chr_pos": "30456342", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1142", "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": "rs1913293262", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913293262" }, { "id": "rs1913293262", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1913293262" }, { "id": "rs1913293262", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1913293262" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NKS->SKS).", "chr_id": "17", "chr_pos": "30456343", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1142", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs777580072", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777580072" }, { "id": "rs777580072", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777580072" }, { "id": "rs777580072", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777580072" } ], "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": "17", "chr_pos": "30456342", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1142", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.1128.1128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75976-1.1147.1147", "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": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.1147.1147", "start_pos": 1147, "end_pos": 1147, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ANNHPSMHMGQPSCPNKSDE", "down_seq": "IPGGVMRGAEWHSHLGSMKD", "glycosylation": [ { "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": "Asn1147", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O75976-1.1128.1128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75976-1.1142.1142", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "title": "Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.", "journal": "Nature biotechnology", "date": "2003", "authors": "Zhang H, Li XJ, Martin DB, Aebersold R", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1910983710", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910983710", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1910983710", "url": "https://www.ensembl.org/id/rs1910983710", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1460795208", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460795208", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1460795208", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460795208", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LARELAAGYRRGDPRLVRLL", "down_seq": "TTDVYLLPSLNPDGFERARE", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G08110WX", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G10819WX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G25451PN", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G40926MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G47012YE", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G47518TP", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G60033FS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G60177UT", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLNTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G92135MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "G98611JV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "LLnTTDVYLLPSLNPDGFER", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn172", "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": "Asn172", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "id": "12754519", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/12754519" }, { "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": "rs1910983710", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910983710" }, { "id": "rs1910983710", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1910983710" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->HTT).", "chr_id": "17", "chr_pos": "30379494", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1460795208", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460795208" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->STT).", "chr_id": "17", "chr_pos": "30379495", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1460795208", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1460795208" }, { "id": "rs1460795208", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1460795208" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NTT->TTT).", "chr_id": "17", "chr_pos": "30379495", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NTT->YTT).", "chr_id": "17", "chr_pos": "30379494", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N172", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.174.174", "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": 29 }, { "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": 28 }, { "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": 28 } ], "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": 28 }, { "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": 28 }, { "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": 28 } ], "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", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.217.217", "start_pos": 217, "end_pos": 217, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs2143288563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143288563", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2143288563", "url": "https://www.ensembl.org/id/rs2143288563", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1434725968", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1434725968", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1434725968", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1434725968#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1434725968", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1434725968", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2143288585", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143288585", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2143288585", "url": "https://www.ensembl.org/id/rs2143288585", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "FGDGGPSGASGRDNSRGRDL", "down_seq": "RSFPDQFSTGEPPALDEVPE", "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": "Asn217", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs2143288563", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143288563" }, { "id": "rs2143288563", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2143288563" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRS->HRS).", "chr_id": "17", "chr_pos": "30379629", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1434725968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1434725968" }, { "id": "rs1434725968", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1434725968#frequency_tab" }, { "id": "rs1434725968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1434725968" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRS->IRS).", "chr_id": "17", "chr_pos": "30379630", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2143288585", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143288585" }, { "id": "rs2143288585", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2143288585" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRS->KRS).", "chr_id": "17", "chr_pos": "30379631", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1434725968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1434725968" }, { "id": "rs1434725968", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1434725968#frequency_tab" }, { "id": "rs1434725968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1434725968" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRS->SRS).", "chr_id": "17", "chr_pos": "30379630", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1434725968", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1434725968" }, { "id": "rs1434725968", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1434725968#frequency_tab" }, { "id": "rs1434725968", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1434725968" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NRS->TRS).", "chr_id": "17", "chr_pos": "30379630", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N217", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O75976-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.219.239", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75976-1.226.226", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.219.239", "start_pos": 219, "end_pos": 239, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "SFPDQFSTGEPPALDEVPEVR", "start_aa": "S", "up_seq": "DGGPSGASGRDNSRGRDLNR", "down_seq": "ALIEWIRRNKFVLSGNLHGG", "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": "SFPDQFSTGEPPALDEVPEVR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Ser", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O75976-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75976-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O75976-1.226.226", "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": "O75976-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "rs753491322", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753491322", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753491322", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753491322", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753491322", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753491322#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs753491322", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753491322", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1769234925", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1769234925", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1769234925", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1769234925#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SGRDNSRGRDLNRSFPDQFS", "down_seq": "GEPPALDEVPEVRALIEWIR", "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": "Thr226", "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": "rs753491322", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753491322" }, { "id": "rs753491322", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753491322" }, { "id": "rs753491322", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs753491322#frequency_tab" }, { "id": "rs753491322", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753491322" } ], "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": "30379656", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T226", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1769234925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1769234925" }, { "id": "rs1769234925", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1769234925#frequency_tab" } ], "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": "30379657", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T226", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O75976-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "O75976-1.219.239", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O75976-1.219.219", "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": "O75976-1.318.328", "start_pos": 318, "end_pos": 328, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "KDGITNGAHWY", "start_aa": "K", "up_seq": "NHPIMKTGEPHCPGDEDETF", "down_seq": "DVEGGMQDYNYVWANCFEIT", "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": "KDGITNGAHWY", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Lys", "end_aa": "Tyr", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O75976-1.300.300", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.325.325", "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": "O75976-1.36.57", "start_pos": 36, "end_pos": 57, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "KAEATTTTTSAGAEAAEGQFDR", "start_aa": "K", "up_seq": "LLLLMCLLLLGSSARAAHIK", "down_seq": "YYHEEELESALREAAAAGLP", "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": "KAEATTTTTSAGAEAAEGQFDR", "relation": "attached", "comment": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Lys", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "O75976-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O75976-1.41.41", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O75976-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75976-1.43.43", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O75976-1.44.44", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.45.45", "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": "O75976-1.399.399", "start_pos": 399, "end_pos": 399, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "rs1567874494", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567874494", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1567874494", "url": "https://www.ensembl.org/id/rs1567874494", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KVHIGVKGFVKDSITGSGLE", "down_seq": "ATISVAGINHNITTGRFGDF", "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": "Asn399", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "rs1567874494", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1567874494" }, { "id": "rs1567874494", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1567874494" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NAT->KAT).", "chr_id": "17", "chr_pos": "30421723", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N399", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75976-1.408.408", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O75976-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 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": "O75976-1.408.408", "start_pos": 408, "end_pos": 408, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "VKDSITGSGLENATISVAGI", "down_seq": "HNITTGRFGDFYRLLVPGTY", "glycosylation": [ { "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": "Asn408", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "O75976-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O75976-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.410.410", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.40.40", "start_pos": 40, "end_pos": 40, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] }, { "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": "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": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1910967769", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910967769", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1910967769", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910967769", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MCLLLLGSSARAAHIKKAEA", "down_seq": "TTTTSAGAEAAEGQFDRYYH", "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": "Thr40", "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": "G53434XO", "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": "Thr40", "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": "G57321FI", "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": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr40", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs1910967769", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910967769" }, { "id": "rs1910967769", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910967769" } ], "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": "30379098", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T40", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75976-1.36.57", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.41.41", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.43.43", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75976-1.44.44", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75976-1.45.45", "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": 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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.410.410", "start_pos": 410, "end_pos": 410, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "rs745350591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745350591", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745350591", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745350591", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745350591", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745350591", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DSITGSGLENATISVAGINH", "down_seq": "ITTGRFGDFYRLLVPGTYNL", "glycosylation": [ { "glytoucan_ac": "G74930WP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "DSITGSGLENATISVAGINHNITTGR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn410", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn410", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "rs745350591", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745350591" }, { "id": "rs745350591", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745350591" }, { "id": "rs745350591", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745350591" } ], "glycoeffect": [ "n-glyco-sequon-loss", "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NIT->SIT); n-glyco-sequon-gain (NHN->NHS).", "chr_id": "17", "chr_pos": "30421755", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N410", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75976-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O75976-1.401.401", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.408.408", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O75976-1.429.429", "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": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "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": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] }, { "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": "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "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": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs534156300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534156300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs534156300", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534156300", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs534156300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534156300", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs534156300", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534156300#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs534156300", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534156300", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CLLLLGSSARAAHIKKAEAT", "down_seq": "TTTSAGAEAAEGQFDRYYHE", "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": "Thr41", "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": "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": "Thr41", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "O75976", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75976" } ] }, { "glytoucan_ac": "G53434XO", "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": "Thr41", "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": "G57321FI", "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": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr41", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs534156300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534156300" }, { "id": "rs534156300", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs534156300" }, { "id": "rs534156300", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs534156300" }, { "id": "rs534156300", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs534156300#frequency_tab" }, { "id": "rs534156300", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs534156300" } ], "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": "30379102", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T41", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O75976-1.36.57", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.43.43", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.44.44", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75976-1.45.45", "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": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 4 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 4 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.429.429", "start_pos": 429, "end_pos": 429, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1912275323", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1912275323", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1912275323", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1912275323#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HNITTGRFGDFYRLLVPGTY", "down_seq": "LTVVLTGYMPLTVTNVVVKE", "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": "Asn429", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs1912275323", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1912275323" }, { "id": "rs1912275323", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1912275323#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NLT->YLT).", "chr_id": "17", "chr_pos": "30421811", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "N429", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O75976-1.410.410", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.431.431", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] }, { "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": "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": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1910968078", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910968078", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1910968078", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1910968078#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1910968078", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910968078", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLLLGSSARAAHIKKAEATT", "down_seq": "TTSAGAEAAEGQFDRYYHEE", "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": "Thr42", "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": "G53434XO", "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": "Thr42", "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": "G57321FI", "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": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr42", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs1910968078", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910968078" }, { "id": "rs1910968078", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1910968078#frequency_tab" }, { "id": "rs1910968078", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910968078" } ], "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": "30379105", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O75976-1.36.57", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.41.41", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.43.43", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.44.44", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.45.45", "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": 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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] }, { "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": "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": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs771662331", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771662331", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771662331", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771662331", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs771662331", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771662331", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771662331", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771662331#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771662331", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771662331", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLLGSSARAAHIKKAEATTT", "down_seq": "TSAGAEAAEGQFDRYYHEEE", "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": "Thr43", "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": "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": "Thr43", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "glytoucan_ac": "G57317CE", "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": "Thr43", "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": "G57321FI", "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": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr43", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] } ], "snv": [ { "evidence": [ { "id": "rs771662331", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771662331" }, { "id": "rs771662331", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs771662331" }, { "id": "rs771662331", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771662331" }, { "id": "rs771662331", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771662331#frequency_tab" }, { "id": "rs771662331", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771662331" } ], "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": "30379107", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T43", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.36.57", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.41.41", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.44.44", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.45.45", "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": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 4 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 4 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 4 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 4 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 11 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "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": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1910968247", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910968247", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1910968247", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910968247", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs868687012", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868687012", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs868687012", "url": "https://www.ensembl.org/id/rs868687012", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLGSSARAAHIKKAEATTTT", "down_seq": "SAGAEAAEGQFDRYYHEEEL", "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": "Thr44", "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": "G53434XO", "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": "Thr44", "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": "G57321FI", "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": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr44", "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": "rs1910968247", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910968247" }, { "id": "rs1910968247", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910968247" } ], "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": "30379110", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T44", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs868687012", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs868687012" }, { "id": "rs868687012", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs868687012" } ], "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": "17", "chr_pos": "30379111", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T44", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1910968247", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1910968247" }, { "id": "rs1910968247", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1910968247" } ], "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": "30379110", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T44", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O75976-1.36.57", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75976-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.41.41", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.43.43", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.45.45", "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": 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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.45.45", "start_pos": 45, "end_pos": 45, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "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": "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": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs1326661858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1326661858", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1326661858", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1326661858#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1326661858", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1326661858", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs772949103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772949103", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772949103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772949103", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772949103", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772949103", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LGSSARAAHIKKAEATTTTT", "down_seq": "AGAEAAEGQFDRYYHEEELE", "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": "S", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Ser", "end_aa": "Ser", "residue": "Ser", "site_lbl": "Ser45", "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": "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": "Ser45", "evidence": [ { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "O75976", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75976" } ] }, { "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": "Ser45", "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": "rs1326661858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1326661858" }, { "id": "rs1326661858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1326661858#frequency_tab" }, { "id": "rs1326661858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1326661858" } ], "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": "17", "chr_pos": "30379114", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S45", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1326661858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1326661858" }, { "id": "rs1326661858", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1326661858#frequency_tab" }, { "id": "rs1326661858", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1326661858" } ], "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": "17", "chr_pos": "30379114", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S45", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs772949103", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772949103" }, { "id": "rs772949103", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772949103" }, { "id": "rs772949103", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772949103" } ], "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": "17", "chr_pos": "30379115", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S45", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.36.57", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75976-1.40.40", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75976-1.41.41", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.42.42", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.43.43", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.44.44", "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": 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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "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": 3 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 3 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.487.487", "start_pos": 487, "end_pos": 487, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] } ], "crossref": [ { "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IPDTTEAVSTASTVAIPNIL", "down_seq": "GTSSSYQPIQPKDFHHHHFP", "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": "Ser487", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] } ], "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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": "30422826", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S487", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.489.489", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.490.490", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75976-1.492.492", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.489.489", "start_pos": 489, "end_pos": 489, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] }, { "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": "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": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "23584533", "url": "https://glygen.org/publication/PubMed/23584533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10.1038/emboj.2013.79", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79", "database": "DOI", "categories": [ "Other" ] }, { "id": "rs372959172", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372959172", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372959172", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372959172", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372959172", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372959172#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372959172", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372959172", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1182148002", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1182148002", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1182148002", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1182148002#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DTTEAVSTASTVAIPNILSG", "down_seq": "SSSYQPIQPKDFHHHHFPDM", "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": "Thr489", "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": "Thr489", "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": "G53434XO", "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": "Thr489", "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": "G57321FI", "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": "Data provided by GlycoDomainViewer", "icn3d_view": {}, "start_aa": "Thr", "end_aa": "Thr", "residue": "Thr", "site_lbl": "Thr489", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" }, { "id": "23584533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23584533" }, { "id": "10.1038/emboj.2013.79", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1038/emboj.2013.79" } ] }, { "glytoucan_ac": "G58001LT", "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": "Thr489", "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": "rs372959172", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372959172" }, { "id": "rs372959172", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372959172" }, { "id": "rs372959172", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372959172#frequency_tab" }, { "id": "rs372959172", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372959172" } ], "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": "30422831", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T489", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1182148002", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1182148002" }, { "id": "rs1182148002", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1182148002#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": "17", "chr_pos": "30422832", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T489", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.487.487", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.490.490", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.492.492", "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": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 5 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_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": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 5 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 5 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_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": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.490.490", "start_pos": 490, "end_pos": 490, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Probing the O-glycoproteome of gastric cancer cell lines for biomarker discovery.", "journal": "Molecular & cellular proteomics : MCP", "date": "2015", "authors": "Campos D, Freitas D, Gomes J, Magalhaes A, Steentoft C, Gomes C, Vester-Christensen MB, Ferreira JA, Afonso LP, Santos LL, Pinto de Sousa J, Mandel U, Clausen H, Vakhrushev SY, Reis CA", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380" } ] }, { "title": "Probing the O-Glycoproteome of Gastric Cancer Cell Lines for Biomarker Discovery", "journal": "Molecular & Cellular Proteomics", "date": "2015", "authors": "Campos D., Freitas D., Gomes J., Magalh\u00e3es A., Steentoft C., Gomes C., Vester-Christensen M. B., Ferreira J. A., Afonso L. P., Santos L. L., Pinto de Sousa J., Mandel U., Clausen H., Vakhrushev S. Y., Reis C. A.", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "DOI", "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] } ], "crossref": [ { "id": "25813380", "url": "https://glygen.org/publication/PubMed/25813380", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "10.1074/mcp.M114.046862", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862", "database": "DOI", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTEAVSTASTVAIPNILSGT", "down_seq": "SSYQPIQPKDFHHHHFPDME", "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": "Ser490", "evidence": [ { "id": "25813380", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25813380" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "10.1074/mcp.M114.046862", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1074/mcp.M114.046862" } ] } ], "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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: o-glyco-site-loss (S->L).", "chr_id": "17", "chr_pos": "30422835", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S490", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O75976-1.487.487", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.489.489", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.492.492", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.522.522", "start_pos": 522, "end_pos": 522, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "HHHHFPDMEIFLRRFANEYP", "down_seq": "ITRLYSLGKSVESRELYVME", "glycosylation": [ { "glytoucan_ac": "G08290VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G10256JP", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G25451PN", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G47012YE", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G60177UT", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G70375MX", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "RFANEYPNITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G81263BG", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G83229XP", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G92135MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FANEYPnITR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn522", "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": "G95133RI", "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": "Asn522", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "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": "Asn522", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.520.520", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75976-1.528.528", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.532.532", "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": 25 }, { "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": 24 }, { "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": 24 } ], "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": 24 }, { "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": 24 }, { "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": 24 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.528.528", "start_pos": 528, "end_pos": 528, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DMEIFLRRFANEYPNITRLY", "down_seq": "LGKSVESRELYVMEISDNPG", "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": "Ser528", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "O75976", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75976" } ] } ], "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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": "30422949", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S528", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O75976-1.520.520", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75976-1.522.522", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75976-1.532.532", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.532.532", "start_pos": 532, "end_pos": 532, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FLRRFANEYPNITRLYSLGK", "down_seq": "VESRELYVMEISDNPGVHEP", "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": "Ser532", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "O75976", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75976" } ] } ], "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1557", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "17", "chr_pos": "30422961", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S532", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.520.520", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O75976-1.522.522", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75976-1.528.528", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.626.626", "start_pos": 626, "end_pos": 626, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "MNPDGYEKSQEGDSISVIGR", "down_seq": "NSNNFDLNRNFPDQFVQITD", "glycosylation": [ { "glytoucan_ac": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "G12313PD", "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": "Asn626", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G18647XP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G37399XV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "G39188ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G39446WN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "G41840AI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "G59924QI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "G82463GQ", "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": "Asn626", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "NNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "G87661QW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "nNSNNFDLNR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn626", "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": "Asn626", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.628.628", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.638.638", "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": 22 }, { "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": 21 }, { "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": 21 } ], "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": 21 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 21 }, { "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": 21 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.628.628", "start_pos": 628, "end_pos": 628, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs372336205", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372336205", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372336205", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372336205", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372336205", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372336205#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372336205", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372336205", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDGYEKSQEGDSISVIGRNN", "down_seq": "NNFDLNRNFPDQFVQITDPT", "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": "Ser628", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "O75976", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/O75976" } ] } ], "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NNS->NNG); o-glyco-site-loss (S->G).", "chr_id": "17", "chr_pos": "30427423", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S628", "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": "rs372336205", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372336205" }, { "id": "rs372336205", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372336205" }, { "id": "rs372336205", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372336205#frequency_tab" }, { "id": "rs372336205", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372336205" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 2 filters: n-glyco-sequon-loss (NNS->NNN); o-glyco-site-loss (S->N).", "chr_id": "17", "chr_pos": "30427424", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S628", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.626.626", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.638.638", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.652.652", "start_pos": 652, "end_pos": 652, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DLNRNFPDQFVQITDPTQPE", "down_seq": "IAVMSWMKSYPFVLSANLHG", "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": "Thr652", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.638.638", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.690.690", "start_pos": 690, "end_pos": 690, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LHGGSLVVNYPFDDDEQGLA", "down_seq": "YSKSPDDAVFQQIALSYSKE", "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": "Thr690", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.711.711", "start_pos": 711, "end_pos": 711, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "YSKSPDDAVFQQIALSYSKE", "down_seq": "SQMFQGRPCKNMYPNEYFPH", "glycosylation": [ { "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": "Asn711", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "O75976-1.728.728", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.811.811", "start_pos": 811, "end_pos": 811, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.", "journal": "Nature biotechnology", "date": "2003", "authors": "Zhang H, Li XJ, Martin DB, Aebersold R", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QVHQGVRGFVLDATDGRGIL", "down_seq": "ATISVAEINHPVTTYKTGDY", "glycosylation": [ { "glytoucan_ac": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G02886BB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "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": "Asn811", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G10486CT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G11314AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G18647XP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G28541PG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G31936TA", "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": "Asn811", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G49018RC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G59924QI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILNATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G83646BJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "G95865ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GILnATISVAEINHPVTTYK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn811", "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": "Asn811", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "12754519", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/12754519" }, { "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.813.813", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O75976-1.824.824", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75976-1.825.825", "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": 24 }, { "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": 23 }, { "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": 23 } ], "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": 23 }, { "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": 23 }, { "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": 23 } ], "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": "O75976-1.824.824", "start_pos": 824, "end_pos": 824, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1912947431", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1912947431", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1912947431", "url": "https://www.ensembl.org/id/rs1912947431", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TDGRGILNATISVAEINHPV", "down_seq": "TYKTGDYWRLLVPGTYKITA", "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": "Thr824", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "snv": [ { "evidence": [ { "id": "rs1912947431", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1912947431" }, { "id": "rs1912947431", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1912947431" } ], "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": "30443899", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T824", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "17", "chr_pos": "30443899", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T824", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O75976-1.811.811", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O75976-1.813.813", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.825.825", "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", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.825.825", "start_pos": 825, "end_pos": 825, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "database": "O-GlcNAc Atlas", "id": "O75976", "url": "https://oglcnac.org/atlas/detail/O75976" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "crossref": [ { "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DGRGILNATISVAEINHPVT", "down_seq": "YKTGDYWRLLVPGTYKITAS", "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": "Thr825", "evidence": [ { "id": "29351928", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29351928" }, { "id": "O75976", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75976" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "37340703", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37340703" }, { "id": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.811.811", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O75976-1.813.813", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.824.824", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.855.855", "start_pos": 855, "end_pos": 855, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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" } ] }, { "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": "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LVPGTYKITASARGYNPVTK", "down_seq": "VTVKSEGAIQVNFTLVRSST", "glycosylation": [ { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GYNPVTKNVTVK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn855", "evidence": [ { "id": "10.1101/2023.09.13.557529", "database": "DOI", "url": "https://glygen.org/publication/DOI/10.1101/2023.09.13.557529" }, { "id": "GLY_000888", "database": "Data Submission", "url": "http://data.glygen.org/GLY_000888" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) asparagine", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn855", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.857.857", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.867.867", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75976-1.869.869", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 2 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 1 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.867.867", "start_pos": 867, "end_pos": 867, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1354303826", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1354303826", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1354303826", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1354303826#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1354303826", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1354303826", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1354303826", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1354303826", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RGYNPVTKNVTVKSEGAIQV", "down_seq": "FTLVRSSTDSNNESKKGKGA", "glycosylation": [ { "glytoucan_ac": "G01650EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SEGAIQVnFTLVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn867", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SEGAIQVnFTLVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn867", "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": "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": "Asn867", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn867", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SEGAIQVNFTLVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn867", "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": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SEGAIQVnFTLVR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn867", "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": "Asn867", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" } ] } ], "snv": [ { "evidence": [ { "id": "rs1354303826", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1354303826" }, { "id": "rs1354303826", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1354303826#frequency_tab" }, { "id": "rs1354303826", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1354303826" }, { "id": "rs1354303826", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1354303826" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NFT->SFT).", "chr_id": "17", "chr_pos": "30445747", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N867", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.855.855", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O75976-1.857.857", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.869.869", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.879.879", "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": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.879.879", "start_pos": 879, "end_pos": 879, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "rs527978533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527978533", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs527978533", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs527978533", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs527978533", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527978533", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs527978533", "url": "https://www.ncbi.nlm.nih.gov/snp/rs527978533#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs527978533", "url": "http://gnomad.broadinstitute.org/awesome?query=rs527978533", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KSEGAIQVNFTLVRSSTDSN", "down_seq": "ESKKGKGASSSTNDASDPTT", "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": "Asn879", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" } ] } ], "snv": [ { "evidence": [ { "id": "rs527978533", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527978533" }, { "id": "rs527978533", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs527978533" }, { "id": "rs527978533", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs527978533" }, { "id": "rs527978533", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs527978533#frequency_tab" }, { "id": "rs527978533", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs527978533" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NES->SES).", "chr_id": "17", "chr_pos": "30445783", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "N879", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.867.867", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O75976-1.869.869", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O75976-1.894.894", "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": "O75976-1.949.949", "start_pos": 949, "end_pos": 949, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "ALYRYHSYKDLSEFLRGLVM", "down_seq": "YPHITNLTNLGQSTEYRHIW", "glycosylation": [ { "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": "Asn949", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75976-1.938.938", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75976-1.955.955", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75976-1.958.958", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.955.955", "start_pos": 955, "end_pos": 955, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Reanalysis of Global Proteomic and Phosphoproteomic Data Identified a Large Number of Glycopeptides.", "journal": "Analytical chemistry", "date": "2018", "authors": "Hu Y, Shah P, Clark DJ, Ao M, Zhang H", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ], "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" } ] }, { "title": "Glycoproteomics analysis of human liver tissue by combination of multiple enzyme digestion and hydrazide chemistry.", "journal": "Journal of proteome research", "date": "2009", "authors": "Chen R, Jiang X, Sun D, Han G, Wang F, Ye M, Wang L, Zou H", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218" } ] }, { "title": "Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry.", "journal": "Nature biotechnology", "date": "2003", "authors": "Zhang H, Li XJ, Martin DB, Aebersold R", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519" } ] }, { "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": "37074911", "url": "https://glygen.org/publication/PubMed/37074911", "database": "PubMed", "categories": [ "Other" ] }, { "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471", "database": "PDC", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "1066", "url": "https://glyconnect.expasy.org/browser/proteins/1066", "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "19159218", "url": "https://glygen.org/publication/PubMed/19159218", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12754519", "url": "https://glygen.org/publication/PubMed/12754519", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1913019747", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913019747", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1913019747", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1913019747#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1913019747", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1913019747", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SYKDLSEFLRGLVMNYPHIT", "down_seq": "LTNLGQSTEYRHIWSLEISN", "glycosylation": [ { "glytoucan_ac": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GLVMNYPHITnLTNLGQSTEYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn955", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G06110VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn955", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "1066", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/1066" } ] }, { "glytoucan_ac": "G15664MX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GLVMNYPHITnLTNLGQSTEYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn955", "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": "GLVMNYPHITNLTNLGQSTEYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn955", "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": "G72747WU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "GLVMNYPHITnLTNLGQSTEYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn955", "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": "GLVMNYPHITnLTNLGQSTEYR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn955", "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": "Asn955", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#ptm_processing" }, { "id": "19159218", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19159218" }, { "id": "12754519", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/12754519" }, { "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": "rs1913019747", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913019747" }, { "id": "rs1913019747", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1913019747#frequency_tab" }, { "id": "rs1913019747", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1913019747" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "sequence_org": "N", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-loss (NLT->DLT).", "chr_id": "17", "chr_pos": "30446010", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N955", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75976-1.938.938", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75976-1.949.949", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.958.958", "categories": [ "glycosylation_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 7 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 6 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 6 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_n_linked_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_n_linked_glycans", "count": 6 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "O75976-1.958.958", "start_pos": 958, "end_pos": 958, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DLSEFLRGLVMNYPHITNLT", "down_seq": "LGQSTEYRHIWSLEISNKPN", "glycosylation": [ { "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": "Asn958", "evidence": [ { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75976-1.938.938", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O75976-1.949.949", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.955.955", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O75976-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75976-1.978.978", "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": 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": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "O75976-1.978.978", "start_pos": 978, "end_pos": 978, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "rs1286804435", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1286804435", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1286804435", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1286804435#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1286804435", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1286804435", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NLGQSTEYRHIWSLEISNKP", "down_seq": "VSEPEEPKIRFVAGIHGNAP", "glycosylation": [ { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "G20706XG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "G27915IV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "HIWSLEISNKPNVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "G65000LJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "HIWSLEISNKPnVSEPEEPK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn978", "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": "Asn978", "evidence": [ { "id": "O75976", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/O75976#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": "rs1286804435", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1286804435" }, { "id": "rs1286804435", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1286804435#frequency_tab" }, { "id": "rs1286804435", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1286804435" } ], "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": "17", "chr_pos": "30449612", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N978", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75976-1.958.958", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.980.980", "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": 11 }, { "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": 10 }, { "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": 10 } ], "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": 10 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 1 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 1 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 10 }, { "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": 10 } ], "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": "O75976-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An alternate receptor for adeno-associated viruses.", "journal": "Cell", "date": "2025-09-04", "authors": "Dhungel Bijay P, Xu Hua, Nagarajah Rajini, Vitale Joseph, Wong Alex C H, Gokal Divya, Feng Yue, Tabar Mehdi Sharifi, Metierre Cynthia, Parsania Chirag, Song Xiaohui, Wang Guopeng, Su Xiao-Dong, Bailey Charles G, Rasko John E J", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "40664211", "url": "https://glygen.org/publication/PubMed/40664211" } ] }, { "title": "Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains.", "journal": "PloS one", "date": "2017", "authors": "Garcia-Pardo Javier, Tanco Sebastian, D\u00edaz Luc\u00eda, Dasgupta Sayani, Fernandez-Recio Juan, Lorenzo Julia, Aviles Francesc X, Fricker Lloyd D", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "29131831", "url": "https://glygen.org/publication/PubMed/29131831" } ] } ], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40664211", "url": "https://glygen.org/publication/PubMed/40664211", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29131831", "url": "https://glygen.org/publication/PubMed/29131831", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VEGGMQDYNYVWANCFEITL", "down_seq": "LSCCKYPPASQLRQEWENNR", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "Q", "comment": "Enzymatically inactive; when associated with Q-762.", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "PubMed", "id": "40664211", "url": "https://glygen.org/publication/PubMed/40664211" }, { "database": "PubMed", "id": "29131831", "url": "https://glygen.org/publication/PubMed/29131831" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "O75976-1.370.370", "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": "O75976-1.762.762", "start_pos": 762, "end_pos": 762, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An alternate receptor for adeno-associated viruses.", "journal": "Cell", "date": "2025-09-04", "authors": "Dhungel Bijay P, Xu Hua, Nagarajah Rajini, Vitale Joseph, Wong Alex C H, Gokal Divya, Feng Yue, Tabar Mehdi Sharifi, Metierre Cynthia, Parsania Chirag, Song Xiaohui, Wang Guopeng, Su Xiao-Dong, Bailey Charles G, Rasko John E J", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "40664211", "url": "https://glygen.org/publication/PubMed/40664211" } ] }, { "title": "Substrate specificity of human metallocarboxypeptidase D: Comparison of the two active carboxypeptidase domains.", "journal": "PloS one", "date": "2017", "authors": "Garcia-Pardo Javier, Tanco Sebastian, D\u00edaz Luc\u00eda, Dasgupta Sayani, Fernandez-Recio Juan, Lorenzo Julia, Aviles Francesc X, Fricker Lloyd D", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "reference": [ { "type": "PubMed", "id": "29131831", "url": "https://glygen.org/publication/PubMed/29131831" } ] } ], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "40664211", "url": "https://glygen.org/publication/PubMed/40664211", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29131831", "url": "https://glygen.org/publication/PubMed/29131831", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VPGGMQDWNYLQTNCFEVTI", "down_seq": "LGCVKYPLEKELPNFWEQNR", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "Q", "comment": "Enzymatically inactive; when associated with Q-350.", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "PubMed", "id": "40664211", "url": "https://glygen.org/publication/PubMed/40664211" }, { "database": "PubMed", "id": "29131831", "url": "https://glygen.org/publication/PubMed/29131831" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "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": "O75976-1.1048.1048", "start_pos": 1048, "end_pos": 1048, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "TRIVIVPSLNPDGRERAQEK", "down_seq": "CTSKIGQTNARGKDLDTDFT", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DCT->NCT).", "chr_id": "17", "chr_pos": "30451783", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D1048", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "O75976-1.1059.1059", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.1059.1059", "start_pos": 1059, "end_pos": 1059, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1430642075", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1430642075", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1430642075", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1430642075#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1430642075", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1430642075", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DGRERAQEKDCTSKIGQTNA", "down_seq": "GKDLDTDFTNNASQPETKAI", "snv": [ { "evidence": [ { "id": "rs1430642075", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1430642075" }, { "id": "rs1430642075", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1430642075#frequency_tab" }, { "id": "rs1430642075", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1430642075" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NAR->NAC).", "chr_id": "17", "chr_pos": "30451816", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R1059", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75976-1.1048.1048", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.1069.1069", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O75976-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.1071.1071", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O75976-1.1072.1072", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.1071.1071", "start_pos": 1071, "end_pos": 1071, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs558201013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558201013", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs558201013", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558201013", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs558201013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558201013", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs558201013", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558201013", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SKIGQTNARGKDLDTDFTNN", "down_seq": "SQPETKAIIENLIQKQDFSL", "snv": [ { "evidence": [ { "id": "rs558201013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558201013" }, { "id": "rs558201013", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558201013" }, { "id": "rs558201013", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558201013" }, { "id": "rs558201013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558201013" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNA->NNS).", "chr_id": "17", "chr_pos": "30455344", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A1071", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs558201013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558201013" }, { "id": "rs558201013", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs558201013" }, { "id": "rs558201013", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs558201013" }, { "id": "rs558201013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs558201013" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NNA->NNT).", "chr_id": "17", "chr_pos": "30455344", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "A1071", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.1059.1059", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.1069.1069", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.1072.1072", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "O75976-1.1072.1072", "start_pos": 1072, "end_pos": 1072, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1367907867", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367907867", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1367907867", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1367907867#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1367907867", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1367907867", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KIGQTNARGKDLDTDFTNNA", "down_seq": "QPETKAIIENLIQKQDFSLS", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs1367907867", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1367907867" }, { "id": "rs1367907867", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1367907867#frequency_tab" }, { "id": "rs1367907867", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1367907867" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAS->NAP).", "chr_id": "17", "chr_pos": "30455347", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S1072", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "O75976-1.1059.1059", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.1069.1069", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.1070.1070", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75976-1.1071.1071", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.1128.1128", "start_pos": 1128, "end_pos": 1128, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KPVQTVENKETLKHLASLYA", "down_seq": "NHPSMHMGQPSCPNKSDENI", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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": "17", "chr_pos": "30456301", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N1128", "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": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "O75976-1.1142.1142", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "O75976-1.1147.1147", "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": "O75976-1.1366.1366", "start_pos": 1366, "end_pos": 1366, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779144998", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779144998", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779144998", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779144998", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779144998", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779144998#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779144998", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779144998", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DEIRMMSTGSKKSLLSHEFQ", "down_seq": "ETDTEEETLYSSKH", "snv": [ { "evidence": [ { "id": "rs779144998", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779144998" }, { "id": "rs779144998", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779144998" }, { "id": "rs779144998", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779144998#frequency_tab" }, { "id": "rs779144998", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779144998" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DET->NET).", "chr_id": "17", "chr_pos": "30464767", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1366", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "O75976-1.1358.1358", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "O75976-1.1361.1361", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.1368.1368", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75976-1.1370.1370", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.1376.1376", "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": "O75976-1.174.174", "start_pos": 174, "end_pos": 174, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs370241648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370241648", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs370241648", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370241648", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs370241648", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370241648#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs370241648", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370241648", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RELAAGYRRGDPRLVRLLNT", "down_seq": "DVYLLPSLNPDGFERAREGD", "snv": [ { "evidence": [ { "id": "rs370241648", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370241648" }, { "id": "rs370241648", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs370241648" }, { "id": "rs370241648", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs370241648#frequency_tab" }, { "id": "rs370241648", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs370241648" } ], "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 (NTT->NTI).", "chr_id": "17", "chr_pos": "30379501", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T174", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.172.172", "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": "O75976-1.212.212", "start_pos": 212, "end_pos": 212, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1451733449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451733449", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1451733449", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451733449#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1451733449", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451733449", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EGDCGFGDGGPSGASGRDNS", "down_seq": "GRDLNRSFPDQFSTGEPPAL", "snv": [ { "evidence": [ { "id": "rs1451733449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451733449" }, { "id": "rs1451733449", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451733449#frequency_tab" }, { "id": "rs1451733449", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451733449" } ], "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": "30379614", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R212", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1451733449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1451733449" }, { "id": "rs1451733449", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1451733449#frequency_tab" }, { "id": "rs1451733449", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1451733449" } ], "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": "30379614", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R212", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O75976-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75976-1.219.239", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75976-1.219.219", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75976-1.226.226", "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": "O75976-1.219.219", "start_pos": 219, "end_pos": 219, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs755815841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755815841", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs755815841", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755815841", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs755815841", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755815841", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DGGPSGASGRDNSRGRDLNR", "down_seq": "FPDQFSTGEPPALDEVPEVR", "snv": [ { "evidence": [ { "id": "rs755815841", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755815841" }, { "id": "rs755815841", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs755815841" }, { "id": "rs755815841", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs755815841" } ], "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 (NRS->NRN).", "chr_id": "17", "chr_pos": "30379636", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S219", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "O75976-1.212.212", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.217.217", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "downstream", "id": "O75976-1.219.239", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75976-1.226.226", "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": "O75976-1.280.280", "start_pos": 280, "end_pos": 280, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768738088", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768738088", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768738088", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768738088", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SVVASYPFDDSPEHKATGIY", "down_seq": "KTSDDEVFKYLAKAYASNHP", "snv": [ { "evidence": [ { "id": "rs768738088", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768738088" }, { "id": "rs768738088", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768738088" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SKT->NKT).", "chr_id": "17", "chr_pos": "30385081", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S280", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O75976-1.265.265", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O75976-1.270.270", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75976-1.300.300", "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": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.300.300", "start_pos": 300, "end_pos": 300, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775540183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775540183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775540183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775540183", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775540183", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775540183#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775540183", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775540183", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "SKTSDDEVFKYLAKAYASNH", "down_seq": "IMKTGEPHCPGDEDETFKDG", "snv": [ { "evidence": [ { "id": "rs775540183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775540183" }, { "id": "rs775540183", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775540183" }, { "id": "rs775540183", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775540183#frequency_tab" }, { "id": "rs775540183", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775540183" } ], "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": "17", "chr_pos": "30385140", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P300", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75976-1.280.280", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O75976-1.318.328", "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": "O75976-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373819167", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373819167", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373819167", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373819167#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373819167", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373819167", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs373819167", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373819167", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "GEPHCPGDEDETFKDGITNG", "down_seq": "HWYDVEGGMQDYNYVWANCF", "snv": [ { "evidence": [ { "id": "rs373819167", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373819167" }, { "id": "rs373819167", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373819167#frequency_tab" }, { "id": "rs373819167", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373819167" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGS).", "chr_id": "17", "chr_pos": "30385215", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A325", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs373819167", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373819167" }, { "id": "rs373819167", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373819167#frequency_tab" }, { "id": "rs373819167", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373819167" }, { "id": "rs373819167", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs373819167" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGT).", "chr_id": "17", "chr_pos": "30385215", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A325", "disease": [ { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O75976-1.318.328", "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": 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": "O75976-1.370.370", "start_pos": 370, "end_pos": 370, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs770390469", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770390469", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770390469", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770390469", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770390469", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770390469#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770390469", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770390469", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs770390469", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770390469", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELSCCKYPPASQLRQEWENN", "down_seq": "ESLITLIEKVHIGVKGFVKD", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs770390469", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770390469" }, { "id": "rs770390469", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770390469" }, { "id": "rs770390469", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770390469#frequency_tab" }, { "id": "rs770390469", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770390469" }, { "id": "rs770390469", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs770390469" } ], "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 (NNR->NNC).", "chr_id": "17", "chr_pos": "30420954", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R370", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75976-1.350.350", "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": "O75976-1.401.401", "start_pos": 401, "end_pos": 401, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs190169686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190169686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs190169686", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190169686", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs190169686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190169686", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs190169686", "url": "https://www.ncbi.nlm.nih.gov/snp/rs190169686#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs190169686", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190169686", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HIGVKGFVKDSITGSGLENA", "down_seq": "ISVAGINHNITTGRFGDFYR", "snv": [ { "evidence": [ { "id": "rs190169686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190169686" }, { "id": "rs190169686", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190169686" }, { "id": "rs190169686", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190169686" }, { "id": "rs190169686", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs190169686#frequency_tab" }, { "id": "rs190169686", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190169686" } ], "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 (NAT->NAA).", "chr_id": "17", "chr_pos": "30421727", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T401", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.399.399", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75976-1.408.408", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75976-1.410.410", "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": "O75976-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs915807738", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs915807738", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs915807738", "url": "https://www.ncbi.nlm.nih.gov/snp/rs915807738#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ITTGRFGDFYRLLVPGTYNL", "down_seq": "VVLTGYMPLTVTNVVVKEGP", "snv": [ { "evidence": [ { "id": "rs915807738", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs915807738" }, { "id": "rs915807738", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs915807738#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": "17", "chr_pos": "30421818", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T431", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.429.429", "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": "O75976-1.492.492", "start_pos": 492, "end_pos": 492, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAVSTASTVAIPNILSGTSS", "down_seq": "YQPIQPKDFHHHHFPDMEIF", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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": "17", "chr_pos": "30422841", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S492", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O75976-1.487.487", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.489.489", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.490.490", "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": "O75976-1.520.520", "start_pos": 520, "end_pos": 520, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764785518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764785518", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764785518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764785518", "database": "ExAC", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DFHHHHFPDMEIFLRRFANE", "down_seq": "PNITRLYSLGKSVESRELYV", "snv": [ { "evidence": [ { "id": "rs764785518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764785518" }, { "id": "rs764785518", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764785518" } ], "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 (NEY->NEC).", "chr_id": "17", "chr_pos": "30422925", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y520", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "O75976-1.522.522", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O75976-1.528.528", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.532.532", "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": "O75976-1.638.638", "start_pos": 638, "end_pos": 638, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "DSISVIGRNNSNNFDLNRNF", "down_seq": "DQFVQITDPTQPETIAVMSW", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NFP->NFT).", "chr_id": "17", "chr_pos": "30427453", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P638", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.626.626", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O75976-1.628.628", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "O75976-1.652.652", "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": "O75976-1.728.728", "start_pos": 728, "end_pos": 728, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1448778530", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1448778530", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1448778530", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1448778530", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1448778530", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1448778530", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SKENSQMFQGRPCKNMYPNE", "down_seq": "FPHGITNGASWYNVPGGMQD", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs1448778530", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1448778530" }, { "id": "rs1448778530", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1448778530" }, { "id": "rs1448778530", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1448778530" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NEY->NEC).", "chr_id": "17", "chr_pos": "30439030", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Y728", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75976-1.711.711", "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": "O75976-1.783.783", "start_pos": 783, "end_pos": 783, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1912899965", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1912899965", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1912899965", "url": "https://www.ensembl.org/id/rs1912899965", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LGCVKYPLEKELPNFWEQNR", "down_seq": "SLIQFMKQVHQGVRGFVLDA", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs1912899965", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1912899965" }, { "id": "rs1912899965", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1912899965" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRS).", "chr_id": "17", "chr_pos": "30442426", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R783", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NRR->NRT).", "chr_id": "17", "chr_pos": "30442425", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "R783", "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: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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "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": "O75976-1.813.813", "start_pos": 813, "end_pos": 813, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Immunopeptidomic Analysis Reveals That Deamidated HLA-bound Peptides Arise Predominantly from Deglycosylated Precursors.", "journal": "Molecular & cellular proteomics : MCP", "date": "2020-07", "authors": "Mei Shutao, Ayala Rochelle, Ramarathinam Sri H, Illing Patricia T, Faridi Pouya, Song Jiangning, Purcell Anthony W, Croft Nathan P", "evidence": [ { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "IEDB", "id": "459054", "url": "https://www.iedb.org/epitope/459054" }, { "database": "IEDB", "id": "472014", "url": "https://www.iedb.org/epitope/472014" }, { "database": "IEDB", "id": "1319021", "url": "https://www.iedb.org/epitope/1319021" } ], "reference": [ { "type": "PubMed", "id": "32357974", "url": "https://glygen.org/publication/PubMed/32357974" } ] } ], "crossref": [ { "id": "rs757442695", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757442695", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757442695", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757442695", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757442695", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757442695", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs757442695", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs757442695", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "O75976", "url": "https://www.iedb.org/epitope/O75976", "database": "IEDB", "categories": [ "Other" ] }, { "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32357974", "url": "https://glygen.org/publication/PubMed/32357974", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HQGVRGFVLDATDGRGILNA", "down_seq": "ISVAEINHPVTTYKTGDYWR", "snv": [ { "evidence": [ { "id": "rs757442695", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757442695" }, { "id": "rs757442695", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757442695" }, { "id": "rs757442695", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757442695" }, { "id": "rs757442695", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs757442695" } ], "glycoeffect": [ "n-glyco-sequon-loss", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-loss (NAT->NAI).", "chr_id": "17", "chr_pos": "30443866", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T813", "keywords": [ "ebi", "somatic" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "IEDB", "id": "O75976", "url": "https://www.iedb.org/epitope/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "32357974", "url": "https://glygen.org/publication/PubMed/32357974" } ], "site_lbl": "Thr813" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.811.811", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "O75976-1.824.824", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.825.825", "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": "O75976-1.857.857", "start_pos": 857, "end_pos": 857, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1913008534", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913008534", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1913008534", "url": "https://www.ensembl.org/id/rs1913008534", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PGTYKITASARGYNPVTKNV", "down_seq": "VKSEGAIQVNFTLVRSSTDS", "snv": [ { "evidence": [ { "id": "rs1913008534", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913008534" }, { "id": "rs1913008534", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1913008534" } ], "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": "17", "chr_pos": "30445717", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T857", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "O75976-1.855.855", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.867.867", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.869.869", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.869.869", "start_pos": 869, "end_pos": 869, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1482172272", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482172272", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1482172272", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1482172272#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "YNPVTKNVTVKSEGAIQVNF", "down_seq": "LVRSSTDSNNESKKGKGASS", "snv": [ { "evidence": [ { "id": "rs1482172272", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482172272" }, { "id": "rs1482172272", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1482172272#frequency_tab" } ], "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 (NFT->NFR).", "chr_id": "17", "chr_pos": "30445753", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T869", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.855.855", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "O75976-1.857.857", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.867.867", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.879.879", "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": "O75976-1.894.894", "start_pos": 894, "end_pos": 894, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1913013658", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913013658", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1913013658", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1913013658", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "STDSNNESKKGKGASSSTND", "down_seq": "SDPTTKEFETLIKDLSAENG", "snv": [ { "evidence": [ { "id": "rs1913013658", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913013658" }, { "id": "rs1913013658", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1913013658" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDA->NDS).", "chr_id": "17", "chr_pos": "30445827", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A894", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "O75976-1.879.879", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "O75976-1.910.910", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.910.910", "start_pos": 910, "end_pos": 910, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STNDASDPTTKEFETLIKDL", "down_seq": "AENGLESLMLRSSSNLALAL", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "30445876", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S910", "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: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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "O75976-1.894.894", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.938.938", "start_pos": 938, "end_pos": 938, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1913018396", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913018396", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1913018396", "url": "https://www.ensembl.org/id/rs1913018396", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1913018396", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1913018396", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LMLRSSSNLALALYRYHSYK", "down_seq": "LSEFLRGLVMNYPHITNLTN", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" }, { "id": "rs1913018396", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1913018396" }, { "id": "rs1913018396", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1913018396" }, { "id": "rs1913018396", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1913018396" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DLS->NLS).", "chr_id": "17", "chr_pos": "30445959", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D938", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "O75976-1.949.949", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O75976-1.955.955", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75976-1.958.958", "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": "O75976-1.977.977", "start_pos": 977, "end_pos": 977, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TNLGQSTEYRHIWSLEISNK", "down_seq": "NVSEPEEPKIRFVAGIHGNA", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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 (NKP->NKT).", "chr_id": "17", "chr_pos": "30449608", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P977", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "O75976-1.958.958", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75976-1.978.978", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.980.980", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "O75976-1.980.980", "start_pos": 980, "end_pos": 980, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GQSTEYRHIWSLEISNKPNV", "down_seq": "EPEEPKIRFVAGIHGNAPVG", "snv": [ { "evidence": [ { "id": "O75976", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/O75976" } ], "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 (NVS->NVF).", "chr_id": "17", "chr_pos": "30449618", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S980", "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": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "O75976-1.977.977", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.978.978", "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": "O75976-1.1344.1344", "start_pos": 1344, "end_pos": 1344, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.", "journal": "Cell", "date": "2007", "authors": "Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ] } ], "crossref": [ { "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SIKSNRHKDGFHRLRQHHDE", "down_seq": "EDEIRMMSTGSKKSLLSHEF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ], "site_lbl": "Tyr1344" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "O75976-1.1358.1358", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "O75976-1.1361.1361", "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": "O75976-1.1358.1358", "start_pos": 1358, "end_pos": 1358, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "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": "RQHHDEYEDEIRMMSTGSKK", "down_seq": "LLSHEFQDETDTEEETLYSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1358" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "O75976-1.1344.1344", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75976-1.1361.1361", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O75976-1.1366.1366", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.1368.1368", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "O75976-1.1370.1370", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "O75976-1.1376.1376", "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": "O75976-1.1361.1361", "start_pos": 1361, "end_pos": 1361, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "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": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "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": "HDEYEDEIRMMSTGSKKSLL", "down_seq": "HEFQDETDTEEETLYSSKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1361" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75976-1.1344.1344", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75976-1.1358.1358", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "O75976-1.1366.1366", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75976-1.1368.1368", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75976-1.1370.1370", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O75976-1.1376.1376", "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": "O75976-1.1368.1368", "start_pos": 1368, "end_pos": 1368, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "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": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "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": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "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": "T", "start_aa": "T", "up_seq": "IRMMSTGSKKSLLSHEFQDE", "down_seq": "DTEEETLYSSKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1368" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "O75976-1.1358.1358", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O75976-1.1361.1361", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.1366.1366", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75976-1.1370.1370", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "O75976-1.1376.1376", "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": "O75976-1.1370.1370", "start_pos": 1370, "end_pos": 1370, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "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": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" } ], "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": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "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": "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": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "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": "T", "start_aa": "T", "up_seq": "MMSTGSKKSLLSHEFQDETD", "down_seq": "EEETLYSSKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" }, { "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": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr1370" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "O75976-1.1358.1358", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "O75976-1.1361.1361", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75976-1.1366.1366", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75976-1.1368.1368", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75976-1.1376.1376", "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": "O75976-1.1376.1376", "start_pos": 1376, "end_pos": 1376, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer.", "journal": "Cell", "date": "2007", "authors": "Rikova K, Guo A, Zeng Q, Possemato A, Yu J, Haack H, Nardone J, Lee K, Reeves C, Li Y, Hu Y, Tan Z, Stokes M, Sullivan L, Mitchell J, Wetzel R, Macneill J, Ren JM, Yuan J, Bakalarski CE, Villen J, Kornhauser JM, Smith B, Li D, Zhou X, Gygi SP, Gu TL, Polakiewicz RD, Rush J, Comb MJ", "evidence": [ { "database": "iPTMnet", "id": "O75976-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976-1" } ], "reference": [ { "type": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ] } ], "crossref": [ { "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "KKSLLSHEFQDETDTEEETL", "down_seq": "SSKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "O75976", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75976" }, { "database": "PubMed", "id": "18083107", "url": "https://glygen.org/publication/PubMed/18083107" } ], "site_lbl": "Tyr1376" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O75976-1.1358.1358", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "O75976-1.1361.1361", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "O75976-1.1366.1366", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "O75976-1.1368.1368", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75976-1.1370.1370", "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": "O75976-1.265.265", "start_pos": 265, "end_pos": 265, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "IRRNKFVLSGNLHGGSVVAS", "down_seq": "PFDDSPEHKATGIYSKTSDD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "site_lbl": "Tyr265" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "O75976-1.270.270", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O75976-1.280.280", "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": "O75976-1.270.270", "start_pos": 270, "end_pos": 270, "uniprot_canonical_ac": "O75976-1", "length": 1380, "uniprot_id": "CBPD_HUMAN", "protein_name": "Carboxypeptidase D", "refseq_ac": "NP_001186704", "refseq_name": "carboxypeptidase D isoform 2", "gene_name": "CPD", "gene_names_uniprotkb": "CPD", "gene_names_refseq": "CPD; GP180", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FVLSGNLHGGSVVASYPFDD", "down_seq": "PEHKATGIYSKTSDDEVFKY", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "O75976", "url": "https://www.uniprot.org/uniprotkb/O75976" } ], "site_lbl": "Ser270" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1069", "end_pos": "1069" }, { "start_pos": "1070", "end_pos": "1070" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1147", "end_pos": "1147" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "239" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "318", "end_pos": "328" }, { "start_pos": "36", "end_pos": "57" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "408", "end_pos": "408" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "626", "end_pos": "626" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "652", "end_pos": "652" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "711", "end_pos": "711" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "825", "end_pos": "825" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "949", "end_pos": "949" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "958", "end_pos": "958" }, { "start_pos": "978", "end_pos": "978" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "350", "end_pos": "350" }, { "start_pos": "762", "end_pos": "762" } ] }, { "type": "snv", "site_list": [ { "start_pos": "410", "end_pos": "410" }, { "start_pos": "628", "end_pos": "628" }, { "start_pos": "1048", "end_pos": "1048" }, { "start_pos": "1059", "end_pos": "1059" }, { "start_pos": "1071", "end_pos": "1071" }, { "start_pos": "1072", "end_pos": "1072" }, { "start_pos": "1128", "end_pos": "1128" }, { "start_pos": "1142", "end_pos": "1142" }, { "start_pos": "1366", "end_pos": "1366" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "174", "end_pos": "174" }, { "start_pos": "212", "end_pos": "212" }, { "start_pos": "217", "end_pos": "217" }, { "start_pos": "219", "end_pos": "219" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "300", "end_pos": "300" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "370", "end_pos": "370" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "401", "end_pos": "401" }, { "start_pos": "40", "end_pos": "40" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "429", "end_pos": "429" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "45", "end_pos": "45" }, { "start_pos": "487", "end_pos": "487" }, { "start_pos": "489", "end_pos": "489" }, { "start_pos": "490", "end_pos": "490" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "520", "end_pos": "520" }, { "start_pos": "528", "end_pos": "528" }, { "start_pos": "532", "end_pos": "532" }, { "start_pos": "638", "end_pos": "638" }, { "start_pos": "728", "end_pos": "728" }, { "start_pos": "783", "end_pos": "783" }, { "start_pos": "813", "end_pos": "813" }, { "start_pos": "824", "end_pos": "824" }, { "start_pos": "857", "end_pos": "857" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "869", "end_pos": "869" }, { "start_pos": "879", "end_pos": "879" }, { "start_pos": "894", "end_pos": "894" }, { "start_pos": "910", "end_pos": "910" }, { "start_pos": "938", "end_pos": "938" }, { "start_pos": "955", "end_pos": "955" }, { "start_pos": "977", "end_pos": "977" }, { "start_pos": "978", "end_pos": "978" }, { "start_pos": "980", "end_pos": "980" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1344", "end_pos": "1344" }, { "start_pos": "1358", "end_pos": "1358" }, { "start_pos": "1361", "end_pos": "1361" }, { "start_pos": "1368", "end_pos": "1368" }, { "start_pos": "1370", "end_pos": "1370" }, { "start_pos": "1376", "end_pos": "1376" }, { "start_pos": "265", "end_pos": "265" }, { "start_pos": "270", "end_pos": "270" }, { "start_pos": "813", "end_pos": "813" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "O75976-1.265.265", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "O75976-1.280.280", "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": "Q93009-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "database": "O-GlcNAc Atlas", "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "database": "O-GlcNAc Atlas", "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "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": "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": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "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": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LCRVLLDNVENKMKGTCVEG", "down_seq": "IPKLFRGKMVSYIQCKEVDY", "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": "Thr319", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q93009", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "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": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q93009-1.305.305", "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q93009-1.630.630", "start_pos": 630, "end_pos": 630, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "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" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SQTMGFPQDQIRLWPMQARS", "down_seq": "GTKRPAMLDNEADGNKTMIE", "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": "LWPMQARSNGTK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn630", "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" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q93009-1.621.621", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q93009-1.643.643", "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": 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": "Q93009-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "database": "O-GlcNAc Atlas", "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "database": "O-GlcNAc Atlas", "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "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": "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": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "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": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TAEEDMEDDTSWRSEATFQF", "down_seq": "VERFSRLSESVLSPPCFVRN", "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": "Thr74", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q93009", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "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": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "Q93009", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q93009" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q93009-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q93009-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q93009-1.66.66", "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q93009-1.802.802", "start_pos": 802, "end_pos": 802, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "35083852", "url": "https://glygen.org/publication/PubMed/35083852" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "database": "O-GlcNAc Atlas", "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "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": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "database": "O-GlcNAc Atlas", "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "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": "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": "35083852", "url": "https://glygen.org/publication/PubMed/35083852", "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": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "https://oglcnac.org/atlas/detail/Q93009", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs758501837", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758501837", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758501837", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758501837", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758501837", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758501837", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TAKEYFRDLYHRVDVIFCDK", "down_seq": "IPNDPGFVVTLSNRMNYFQV", "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": "Thr802", "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q93009", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q93009" }, { "id": "32119511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32119511" }, { "id": "30397120", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30397120" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "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": "35083852", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35083852" }, { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "Q93009", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q93009" } ] } ], "snv": [ { "evidence": [ { "id": "rs758501837", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758501837" }, { "id": "rs758501837", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758501837" }, { "id": "rs758501837", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758501837" } ], "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": "16", "chr_pos": "8899662", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T802", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q93009-1.820.820", "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": 14 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q93009-1.164.164", "start_pos": 164, "end_pos": 164, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular recognition of p53 and MDM2 by USP7/HAUSP.", "journal": "Nature structural & molecular biology", "date": "2006", "authors": "Sheng Y, Saridakis V, Sarkari F, Duan S, Wu T, Arrowsmith CH, Frappier L", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "Reactome", "id": "R-HSA-6804757", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6804757" } ], "reference": [ { "type": "PubMed", "id": "16474402", "url": "https://glygen.org/publication/PubMed/16474402" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16474402", "url": "https://glygen.org/publication/PubMed/16474402", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "RDDEKSFSRRISHLFFHKEN", "down_seq": "WGFSNFMAWSEVTDPEKGFI", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Decreased binding to p53/TP53 and MDM2.", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "16474402", "url": "https://glygen.org/publication/PubMed/16474402" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q93009-1.165.165", "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": "Q93009-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Molecular recognition of p53 and MDM2 by USP7/HAUSP.", "journal": "Nature structural & molecular biology", "date": "2006", "authors": "Sheng Y, Saridakis V, Sarkari F, Duan S, Wu T, Arrowsmith CH, Frappier L", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "Reactome", "id": "R-HSA-6804757", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6804757" } ], "reference": [ { "type": "PubMed", "id": "16474402", "url": "https://glygen.org/publication/PubMed/16474402" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16474402", "url": "https://glygen.org/publication/PubMed/16474402", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "DDEKSFSRRISHLFFHKEND", "down_seq": "GFSNFMAWSEVTDPEKGFID", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "Loss of binding to p53/TP53 and MDM2.", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "16474402", "url": "https://glygen.org/publication/PubMed/16474402" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q93009-1.164.164", "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": "Q93009-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Deubiquitination of p53 by HAUSP is an important pathway for p53 stabilization.", "journal": "Nature", "date": "2002", "authors": "Li M, Chen D, Shiloh A, Luo J, Nikolaev AY, Qin J, Gu W", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "Reactome", "id": "R-HSA-6804757", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6804757" } ], "reference": [ { "type": "PubMed", "id": "11923872", "url": "https://glygen.org/publication/PubMed/11923872" } ] }, { "title": "M phase phosphorylation of the epigenetic regulator UHRF1 regulates its physical association with the deubiquitylase USP7 and stability.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2012", "authors": "Ma H, Chen H, Guo X, Wang Z, Sowa ME, Zheng L, Hu S, Zeng P, Guo R, Diao J, Lan F, Harper JW, Shi YG, Xu Y, Shi Y", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "22411829", "url": "https://glygen.org/publication/PubMed/22411829" } ] }, { "title": "FOXO4 transcriptional activity is regulated by monoubiquitination and USP7/HAUSP.", "journal": "Nature cell biology", "date": "2006", "authors": "van der Horst A, de Vries-Smits AM, Brenkman AB, van Triest MH, van den Broek N, Colland F, Maurice MM, Burgering BM", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "Reactome", "id": "R-HSA-5689880", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5689880" } ], "reference": [ { "type": "PubMed", "id": "16964248", "url": "https://glygen.org/publication/PubMed/16964248" } ] }, { "title": "The deubiquitinylation and localization of PTEN are regulated by a HAUSP-PML network.", "journal": "Nature", "date": "2008", "authors": "Song MS, Salmena L, Carracedo A, Egia A, Lo-Coco F, Teruya-Feldstein J, Pandolfi PP", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "Reactome", "id": "R-HSA-8948747", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-8948747" } ], "reference": [ { "type": "PubMed", "id": "18716620", "url": "https://glygen.org/publication/PubMed/18716620" } ] }, { "title": "The USP7/Dnmt1 complex stimulates the DNA methylation activity of Dnmt1 and regulates the stability of UHRF1.", "journal": "Nucleic acids research", "date": "2011", "authors": "Felle M, Joppien S, Nemeth A, Diermeier S, Thalhammer V, Dobner T, Kremmer E, Kappler R, Langst G", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "21745816", "url": "https://glygen.org/publication/PubMed/21745816" } ] }, { "title": "USP7 and TDP-43: Pleiotropic Regulation of Cryptochrome Protein Stability Paces the Oscillation of the Mammalian Circadian Clock.", "journal": "PloS one", "date": "2016", "authors": "Hirano A, Nakagawa T, Yoshitane H, Oyama M, Kozuka-Hata H, Lanjakornsiripan D, Fukada Y", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "27123980", "url": "https://glygen.org/publication/PubMed/27123980" } ] }, { "title": "Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.", "journal": "Cell", "date": "2002", "authors": "Hu M, Li P, Li M, Li W, Yao T, Wu JW, Gu W, Cohen RE, Shi Y", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" } ] }, { "title": "A dynamic role of HAUSP in the p53-Mdm2 pathway.", "journal": "Molecular cell", "date": "2004", "authors": "Li M, Brooks CL, Kon N, Gu W", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "Reactome", "id": "R-HSA-6804757", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-6804757" } ], "reference": [ { "type": "PubMed", "id": "15053880", "url": "https://glygen.org/publication/PubMed/15053880" } ] }, { "title": "USP7 Acts as a Molecular Rheostat to Promote WASH-Dependent Endosomal Protein Recycling and Is Mutated in a Human Neurodevelopmental Disorder.", "journal": "Molecular cell", "date": "2015", "authors": "Hao YH, Fountain MD Jr, Fon Tacer K, Xia F, Bi W, Kang SH, Patel A, Rosenfeld JA, Le Caignec C, Isidor B, Krantz ID, Noon SE, Pfotenhauer JP, Morgan TM, Moran R, Pedersen RC, Saenz MS, Schaaf CP, Potts PR", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "RefSeq", "id": "NP_001308787", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001308787" } ], "reference": [ { "type": "PubMed", "id": "26365382", "url": "https://glygen.org/publication/PubMed/26365382" } ] }, { "title": "Noncanonical regulation of alkylation damage resistance by the OTUD4 deubiquitinase.", "journal": "The EMBO journal", "date": "2015", "authors": "Zhao Y, Majid MC, Soll JM, Brickner JR, Dango S, Mosammaparast N", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "25944111", "url": "https://glygen.org/publication/PubMed/25944111" } ] }, { "title": "Deubiquitylase HAUSP stabilizes REST and promotes maintenance of neural progenitor cells.", "journal": "Nature cell biology", "date": "2011", "authors": "Huang Z, Wu Q, Guryanova OA, Cheng L, Shou W, Rich JN, Bao S", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "21258371", "url": "https://glygen.org/publication/PubMed/21258371" } ] }, { "title": "Mixed Lineage Leukemia 5 (MLL5) Protein Stability Is Cooperatively Regulated by O-GlcNac Transferase (OGT) and Ubiquitin Specific Protease 7 (USP7).", "journal": "PloS one", "date": "2015", "authors": "Ding X, Jiang W, Zhou P, Liu L, Wan X, Yuan X, Wang X, Chen M, Chen J, Yang J, Kong C, Li B, Peng C, Wong CC, Hou F, Zhang Y", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "26678539", "url": "https://glygen.org/publication/PubMed/26678539" } ] }, { "title": "Ubiquitin-specific peptidase 7 (USP7)-mediated deubiquitination of the histone deacetylase SIRT7 regulates gluconeogenesis.", "journal": "The Journal of biological chemistry", "date": "2017", "authors": "Jiang L, Xiong J, Zhan J, Yuan F, Tang M, Zhang C, Cao Z, Chen Y, Lu X, Li Y, Wang H, Wang L, Wang J, Zhu WG, Wang H", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "28655758", "url": "https://glygen.org/publication/PubMed/28655758" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11923872", "url": "https://glygen.org/publication/PubMed/11923872", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22411829", "url": "https://glygen.org/publication/PubMed/22411829", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16964248", "url": "https://glygen.org/publication/PubMed/16964248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18716620", "url": "https://glygen.org/publication/PubMed/18716620", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21745816", "url": "https://glygen.org/publication/PubMed/21745816", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27123980", "url": "https://glygen.org/publication/PubMed/27123980", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15053880", "url": "https://glygen.org/publication/PubMed/15053880", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26365382", "url": "https://glygen.org/publication/PubMed/26365382", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25944111", "url": "https://glygen.org/publication/PubMed/25944111", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21258371", "url": "https://glygen.org/publication/PubMed/21258371", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26678539", "url": "https://glygen.org/publication/PubMed/26678539", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28655758", "url": "https://glygen.org/publication/PubMed/28655758", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "VAWDSKKHTGYVGLKNQGAT", "down_seq": "YMNSLLQTLFFTNQLRKAVY", "mutagenesis": [ { "sequence_org": "C", "sequence_mut": "A", "comment": "Complete loss of activity. Localized in the nucleus and does not inhibit FOXO4-dependent transcriptional activity. Loss of ability to deubiquitinate CRY2.", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "11923872", "url": "https://glygen.org/publication/PubMed/11923872" }, { "database": "PubMed", "id": "22411829", "url": "https://glygen.org/publication/PubMed/22411829" }, { "database": "PubMed", "id": "16964248", "url": "https://glygen.org/publication/PubMed/16964248" }, { "database": "PubMed", "id": "18716620", "url": "https://glygen.org/publication/PubMed/18716620" }, { "database": "PubMed", "id": "21745816", "url": "https://glygen.org/publication/PubMed/21745816" }, { "database": "PubMed", "id": "27123980", "url": "https://glygen.org/publication/PubMed/27123980" }, { "database": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" }, { "database": "PubMed", "id": "15053880", "url": "https://glygen.org/publication/PubMed/15053880" } ] }, { "sequence_org": "C", "sequence_mut": "S", "comment": "Catalytically inactive mutant. No effect on p53/TP53 and PTEN binding but is defective in deubiquitinating p53/TP53 and PTEN. Partial loss of KMT2E/mml5 deubiquitination. Decreases deubiquitinase activity toward 'Lys-48'-polyubiquitinated ALKBH3. Reduced deubiquitination of REST. Reduced deubiquitination of TRIM27 and WASHC1.", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "11923872", "url": "https://glygen.org/publication/PubMed/11923872" }, { "database": "PubMed", "id": "22411829", "url": "https://glygen.org/publication/PubMed/22411829" }, { "database": "PubMed", "id": "16964248", "url": "https://glygen.org/publication/PubMed/16964248" }, { "database": "PubMed", "id": "18716620", "url": "https://glygen.org/publication/PubMed/18716620" }, { "database": "PubMed", "id": "21745816", "url": "https://glygen.org/publication/PubMed/21745816" }, { "database": "PubMed", "id": "26365382", "url": "https://glygen.org/publication/PubMed/26365382" }, { "database": "PubMed", "id": "25944111", "url": "https://glygen.org/publication/PubMed/25944111" }, { "database": "PubMed", "id": "21258371", "url": "https://glygen.org/publication/PubMed/21258371" }, { "database": "PubMed", "id": "26678539", "url": "https://glygen.org/publication/PubMed/26678539" }, { "database": "PubMed", "id": "28655758", "url": "https://glygen.org/publication/PubMed/28655758" }, { "database": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" }, { "database": "PubMed", "id": "15053880", "url": "https://glygen.org/publication/PubMed/15053880" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q93009-1.456.456", "start_pos": 456, "end_pos": 456, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.", "journal": "Cell", "date": "2002", "authors": "Hu M, Li P, Li M, Li W, Yao T, Wu JW, Gu W, Cohen RE, Shi Y", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "FLQKTDPKDPANYILHAVLV", "down_seq": "SGDNHGGHYVVYLNPKGDGK", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Complete loss of activity.", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q93009-1.449.449", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q93009-1.464.464", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q93009-1.476.476", "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": "Q93009-1.464.464", "start_pos": 464, "end_pos": 464, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde.", "journal": "Cell", "date": "2002", "authors": "Hu M, Li P, Li M, Li W, Yao T, Wu JW, Gu W, Cohen RE, Shi Y", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "reference": [ { "type": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DPANYILHAVLVHSGDNHGG", "down_seq": "YVVYLNPKGDGKWCKFDDDV", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Complete loss of activity.", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "12507430", "url": "https://glygen.org/publication/PubMed/12507430" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q93009-1.449.449", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q93009-1.456.456", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q93009-1.476.476", "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": "Q93009-1.1018.1018", "start_pos": 1018, "end_pos": 1018, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EVFGTFGIPFLLRIHQGEHF", "down_seq": "EVMKRIQSLLDIQEKEFEKF", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "8894843", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1018", "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: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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q93009-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QTLFFTNQLRKAVYMMPTEG", "down_seq": "DSSKSVPLALQRVFYELQHS", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DDS->NDS).", "chr_id": "16", "chr_pos": "8917129", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D250", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q93009-1.305.305", "start_pos": 305, "end_pos": 305, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "WETLDSFMQHDVQELCRVLL", "down_seq": "NVENKMKGTCVEGTIPKLFR", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "8915519", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D305", "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: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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q93009-1.319.319", "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": "Q93009-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QQLSEPEDMEMEAGDTDDPP", "down_seq": "ITQNPVINGNVALSDGHNTA", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "8930373", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R35", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q93009-1.18.18", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q93009-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q93009-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q93009-1.55.55", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q93009-1.361.361", "start_pos": 361, "end_pos": 361, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs762632614", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762632614", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762632614", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762632614", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "SDRREDYYDIQLSIKGKKNI", "down_seq": "ESFVDYVAVEQLDGDNKYDA", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" }, { "id": "rs762632614", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762632614" }, { "id": "rs762632614", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762632614" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIF->NIS).", "chr_id": "16", "chr_pos": "8910824", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "F361", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q93009-1.369.369", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q93009-1.375.375", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q93009-1.369.369", "start_pos": 369, "end_pos": 369, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DIQLSIKGKKNIFESFVDYV", "down_seq": "VEQLDGDNKYDAGEHGLQEA", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "16", "chr_pos": "8910801", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A369", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q93009-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q93009-1.375.375", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q93009-1.375.375", "start_pos": 375, "end_pos": 375, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KGKKNIFESFVDYVAVEQLD", "down_seq": "DNKYDAGEHGLQEAEKGVKF", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "16", "chr_pos": "8910782", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G375", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q93009-1.361.361", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q93009-1.369.369", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q93009-1.449.449", "start_pos": 449, "end_pos": 449, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748840212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748840212", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748840212", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748840212", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748840212", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748840212", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EQLPLDEFLQKTDPKDPANY", "down_seq": "LHAVLVHSGDNHGGHYVVYL", "snv": [ { "evidence": [ { "id": "rs748840212", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748840212" }, { "id": "rs748840212", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748840212" }, { "id": "rs748840212", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748840212" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYI->NYT).", "chr_id": "16", "chr_pos": "8906508", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I449", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q93009-1.456.456", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q93009-1.464.464", "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": "Q93009-1.476.476", "start_pos": 476, "end_pos": 476, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753320462", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753320462", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753320462", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753320462", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753320462", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753320462", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "HSGDNHGGHYVVYLNPKGDG", "down_seq": "WCKFDDDVVSRCTKEEAIEH", "snv": [ { "evidence": [ { "id": "rs753320462", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753320462" }, { "id": "rs753320462", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753320462" }, { "id": "rs753320462", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753320462" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KWC->NWC).", "chr_id": "16", "chr_pos": "8906426", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K476", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q93009-1.456.456", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q93009-1.464.464", "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": "Q93009-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "AGDTDDPPRITQNPVINGNV", "down_seq": "LSDGHNTAEEDMEDDTSWRS", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVA->NVT).", "chr_id": "16", "chr_pos": "8930338", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A47", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q93009-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q93009-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q93009-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q93009-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q93009-1.66.66", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q93009-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MNH", "down_seq": "QQQQQQKAGEQQLSEPEDME", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "16", "chr_pos": "8963274", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q4", "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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID: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: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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "upstream", "id": "Q93009-1.18.18", "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": "Q93009-1.504.504", "start_pos": 504, "end_pos": 504, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VVSRCTKEEAIEHNYGGHDD", "down_seq": "LSVRHCTNAYMLVYIRESKL", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "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 (DLS->NLS).", "chr_id": "16", "chr_pos": "8905250", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D504", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q93009-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs750227103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750227103", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs750227103", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750227103", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs750227103", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750227103#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs750227103", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750227103", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs750227103", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750227103", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RITQNPVINGNVALSDGHNT", "down_seq": "EEDMEDDTSWRSEATFQFTV", "snv": [ { "evidence": [ { "id": "rs750227103", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750227103" }, { "id": "rs750227103", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs750227103" }, { "id": "rs750227103", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs750227103#frequency_tab" }, { "id": "rs750227103", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs750227103" }, { "id": "rs750227103", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs750227103" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTA->NTT).", "chr_id": "16", "chr_pos": "8930314", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A55", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q93009-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q93009-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q93009-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q93009-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q93009-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q93009-1.74.74", "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": "Q93009-1.571.571", "start_pos": 571, "end_pos": 571, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EAQKRKERQEAHLYMQVQIV", "down_seq": "EDQFCGHQGNDMYDEEKVKY", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "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": "16", "chr_pos": "8903396", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A571", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q93009-1.608.608", "start_pos": 608, "end_pos": 608, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757088246", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757088246", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757088246", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757088246", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757088246", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757088246", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KVKYTVFKVLKNSSLAEFVQ", "down_seq": "LSQTMGFPQDQIRLWPMQAR", "snv": [ { "evidence": [ { "id": "rs757088246", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757088246" }, { "id": "rs757088246", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757088246" }, { "id": "rs757088246", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757088246" } ], "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": "16", "chr_pos": "8903284", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S608", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q93009-1.621.621", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q93009-1.621.621", "start_pos": 621, "end_pos": 621, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SLAEFVQSLSQTMGFPQDQI", "down_seq": "LWPMQARSNGTKRPAMLDNE", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "16", "chr_pos": "8902461", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R621", "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: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" } ] }, { "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q93009-1.608.608", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q93009-1.630.630", "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": "Q93009-1.62.62", "start_pos": 62, "end_pos": 62, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs753015445", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753015445", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs753015445", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753015445", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs753015445", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753015445", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "INGNVALSDGHNTAEEDMED", "down_seq": "TSWRSEATFQFTVERFSRLS", "snv": [ { "evidence": [ { "id": "rs753015445", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753015445" }, { "id": "rs753015445", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs753015445" }, { "id": "rs753015445", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs753015445" } ], "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": "16", "chr_pos": "8930293", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D62", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q93009-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q93009-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q93009-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q93009-1.66.66", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q93009-1.74.74", "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": "Q93009-1.643.643", "start_pos": 643, "end_pos": 643, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "WPMQARSNGTKRPAMLDNEA", "down_seq": "GNKTMIELSDNENPWTIFLE", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "16", "chr_pos": "8902395", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D643", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q93009-1.630.630", "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": "Q93009-1.66.66", "start_pos": 66, "end_pos": 66, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "VALSDGHNTAEEDMEDDTSW", "down_seq": "SEATFQFTVERFSRLSESVL", "snv": [ { "evidence": [ { "id": "Q93009", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q93009" } ], "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": "16", "chr_pos": "8923402", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R66", "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": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q93009-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q93009-1.49.49", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q93009-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q93009-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q93009-1.74.74", "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": "Q93009-1.776.776", "start_pos": 776, "end_pos": 776, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2549220991", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2549220991", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ALDELMDGDIIVFQKDDPEN", "down_seq": "NSELPTAKEYFRDLYHRVDV", "snv": [ { "evidence": [ { "id": "rs2549220991", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2549220991" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DNS->NNS).", "chr_id": "16", "chr_pos": "8899741", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D776", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q93009-1.820.820", "start_pos": 820, "end_pos": 820, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1319085921", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1319085921", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1319085921", "url": "https://www.ensembl.org/id/rs1319085921", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DKTIPNDPGFVVTLSNRMNY", "down_seq": "QVAKTVAQRLNTDPMLLQFF", "snv": [ { "evidence": [ { "id": "rs1319085921", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1319085921" }, { "id": "rs1319085921", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1319085921" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYF->NYC).", "chr_id": "16", "chr_pos": "8899608", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F820", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q93009-1.802.802", "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": "Q93009-1.934.934", "start_pos": 934, "end_pos": 934, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs557701280", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557701280", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs557701280", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557701280", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs557701280", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557701280", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs557701280", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557701280#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs557701280", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557701280", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KHGCVRDLLEECKKAVELGE", "down_seq": "ASGKLRLLEIVSYKIIGVHQ", "snv": [ { "evidence": [ { "id": "rs557701280", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557701280" }, { "id": "rs557701280", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs557701280" }, { "id": "rs557701280", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs557701280" }, { "id": "rs557701280", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs557701280#frequency_tab" }, { "id": "rs557701280", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs557701280" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KAS->NAS).", "chr_id": "16", "chr_pos": "8897016", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "K934", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q93009-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "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": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization.", "journal": "The FEBS journal", "date": "2007", "authors": "Fernandez-Montalvan A, Bouwmeester T, Joberty G, Mader R, Mahnke M, Pierrat B, Schlaeppi JM, Worpenberg S, Gerhartz B", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "17651432", "url": "https://glygen.org/publication/PubMed/17651432" } ] }, { "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": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver phosphoproteome.", "journal": "Journal of proteomics", "date": "2014", "authors": "Bian Y, Song C, Cheng K, Dong M, Wang F, Huang J, Sun D, Wang L, Ye M, Zou H", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] }, { "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "reference": [ { "type": "PubMed", "id": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" } ] }, { "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "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": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] }, { "title": "Phosphoproteomic analysis of primary human multiple myeloma cells.", "journal": "Journal of proteomics", "date": "2010", "authors": "Ge F, Xiao CL, Yin XF, Lu CH, Zeng HL, He QY", "evidence": [ { "database": "iPTMnet", "id": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "reference": [ { "type": "PubMed", "id": "20230923", "url": "https://glygen.org/publication/PubMed/20230923" } ] }, { "title": "ATM-dependent downregulation of USP7/HAUSP by PPM1G activates p53 response to DNA damage.", "journal": "Molecular cell", "date": "2012", "authors": "Khoronenkova SV, Dianova II, Ternette N, Kessler BM, Parsons JL, Dianov GL", "evidence": [ { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "22361354", "url": "https://glygen.org/publication/PubMed/22361354" } ] }, { "title": "HAUSP-nucleolin interaction is regulated by p53-Mdm2 complex in response to DNA damage response.", "journal": "Scientific reports", "date": "2015", "authors": "Lim KH, Park JJ, Gu BH, Kim JO, Park SG, Baek KH", "evidence": [ { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "26238070", "url": "https://glygen.org/publication/PubMed/26238070" } ] }, { "title": "Therapeutic inhibition of USP7-PTEN network in chronic lymphocytic leukemia: a strategy to overcome TP53 mutated/deleted clones.", "journal": "Oncotarget", "date": "2017", "authors": "Carra G, Panuzzo C, Torti D, Parvis G, Crivellaro S, Familiari U, Volante M, Morena D, Lingua MF, Brancaccio M, Guerrasio A, Pandolfi PP, Saglio G, Taulli R, Morotti A", "evidence": [ { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "28418900", "url": "https://glygen.org/publication/PubMed/28418900" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "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": "17651432", "url": "https://glygen.org/publication/PubMed/17651432", "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": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009", "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": "18707149", "url": "https://glygen.org/publication/PubMed/18707149", "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": "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": "20230923", "url": "https://glygen.org/publication/PubMed/20230923", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22361354", "url": "https://glygen.org/publication/PubMed/22361354", "database": "PubMed", "categories": [ "Other" ] }, { "id": "26238070", "url": "https://glygen.org/publication/PubMed/26238070", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28418900", "url": "https://glygen.org/publication/PubMed/28418900", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MNHQQQQQQQKAGEQQL", "down_seq": "EPEDMEMEAGDTDDPPRITQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "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": "17651432", "url": "https://glygen.org/publication/PubMed/17651432" }, { "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": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" }, { "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": "18707149", "url": "https://glygen.org/publication/PubMed/18707149" }, { "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": "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": "20230923", "url": "https://glygen.org/publication/PubMed/20230923" }, { "database": "PubMed", "id": "22361354", "url": "https://glygen.org/publication/PubMed/22361354" }, { "database": "PubMed", "id": "26238070", "url": "https://glygen.org/publication/PubMed/26238070" }, { "database": "PubMed", "id": "28418900", "url": "https://glygen.org/publication/PubMed/28418900" } ], "site_lbl": "Ser18" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q93009-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q93009-1.35.35", "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": 19 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q93009-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "DTDDPPRITQNPVINGNVAL", "down_seq": "DGHNTAEEDMEDDTSWRSEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "site_lbl": "Ser49" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q93009-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q93009-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q93009-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q93009-1.62.62", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q93009-1.66.66", "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": "Q93009-1.963.963", "start_pos": 963, "end_pos": 963, "uniprot_canonical_ac": "Q93009-1", "length": 1102, "uniprot_id": "UBP7_HUMAN", "protein_name": "Ubiquitin C-terminal hydrolase 7", "refseq_ac": "NP_001308787", "refseq_name": "ubiquitin carboxyl-terminal hydrolase 7 isoform 4", "gene_name": "USP7", "gene_names_uniprotkb": "USP7; HAUSP", "gene_names_refseq": "C16DELp13.2; DEL16P13.2; HAFOUS; HAUSP; TEF1; USP7", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" } ], "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": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Biochemical characterization of USP7 reveals post-translational modification sites and structural requirements for substrate processing and subcellular localization.", "journal": "The FEBS journal", "date": "2007", "authors": "Fernandez-Montalvan A, Bouwmeester T, Joberty G, Mader R, Mahnke M, Pierrat B, Schlaeppi JM, Worpenberg S, Gerhartz B", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "reference": [ { "type": "PubMed", "id": "17651432", "url": "https://glygen.org/publication/PubMed/17651432" } ] } ], "crossref": [ { "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "17651432", "url": "https://glygen.org/publication/PubMed/17651432", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EIVSYKIIGVHQEDELLECL", "down_seq": "PATSRTFRIEEIPLDQVDID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q93009", "url": "https://www.uniprot.org/uniprotkb/Q93009" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "17651432", "url": "https://glygen.org/publication/PubMed/17651432" }, { "database": "iPTMnet", "id": "Q93009", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q93009" } ], "site_lbl": "Ser963" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "319", "end_pos": "319" }, { "start_pos": "630", "end_pos": "630" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "802", "end_pos": "802" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "164", "end_pos": "164" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "456", "end_pos": "456" }, { "start_pos": "464", "end_pos": "464" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1018", "end_pos": "1018" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "305", "end_pos": "305" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "375", "end_pos": "375" }, { "start_pos": "449", "end_pos": "449" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "504", "end_pos": "504" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "608", "end_pos": "608" }, { "start_pos": "621", "end_pos": "621" }, { "start_pos": "62", "end_pos": "62" }, { "start_pos": "643", "end_pos": "643" }, { "start_pos": "66", "end_pos": "66" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "820", "end_pos": "820" }, { "start_pos": "934", "end_pos": "934" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "963", "end_pos": "963" } ] } ], "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": "Q7LG56-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q7LG56-1", "length": 351, "uniprot_id": "RIR2B_HUMAN", "protein_name": "Ribonucleoside-diphosphate reductase subunit M2 B", "refseq_ac": "NP_001165948", "refseq_name": "ribonucleoside-diphosphate reductase subunit M2 B isoform 2", "gene_name": "RRM2B", "gene_names_uniprotkb": "RRM2B; P53R2", "gene_names_refseq": "MTDPS8A; MTDPS8B; P53R2; RCDFRD; RRM2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7LG56", "url": "https://www.uniprot.org/uniprotkb/Q7LG56" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q7LG56", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7LG56" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q7LG56", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7LG56", "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": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "Q7LG56", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q7LG56" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "323", "end_pos": "323" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "72", "end_pos": "72" } ] } ], "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": "Q7LG56-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "Q7LG56-1", "length": 351, "uniprot_id": "RIR2B_HUMAN", "protein_name": "Ribonucleoside-diphosphate reductase subunit M2 B", "refseq_ac": "NP_001165948", "refseq_name": "ribonucleoside-diphosphate reductase subunit M2 B isoform 2", "gene_name": "RRM2B", "gene_names_uniprotkb": "RRM2B; P53R2", "gene_names_refseq": "MTDPS8A; MTDPS8B; P53R2; RCDFRD; RRM2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7LG56", "url": "https://www.uniprot.org/uniprotkb/Q7LG56" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q7LG56", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7LG56", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "FQAENPFDFMENISLEGKTN", "down_seq": "FEKRVSEYQRFAVMAETTDN", "snv": [ { "evidence": [ { "id": "Q7LG56", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q7LG56" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "102208220", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "F323", "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: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": "323", "end_pos": "323" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "72", "end_pos": "72" } ] } ], "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": "Q7LG56-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "Q7LG56-1", "length": 351, "uniprot_id": "RIR2B_HUMAN", "protein_name": "Ribonucleoside-diphosphate reductase subunit M2 B", "refseq_ac": "NP_001165948", "refseq_name": "ribonucleoside-diphosphate reductase subunit M2 B isoform 2", "gene_name": "RRM2B", "gene_names_uniprotkb": "RRM2B; P53R2", "gene_names_refseq": "MTDPS8A; MTDPS8B; P53R2; RCDFRD; RRM2B", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q7LG56", "url": "https://www.uniprot.org/uniprotkb/Q7LG56" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "ATM-mediated serine 72 phosphorylation stabilizes ribonucleotide reductase small subunit p53R2 protein against MDM2 to DNA damage.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Chang L, Zhou B, Hu S, Guo R, Liu X, Jones SN, Yen Y", "evidence": [ { "database": "iPTMnet", "id": "Q7LG56", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7LG56" } ], "reference": [ { "type": "PubMed", "id": "19015526", "url": "https://glygen.org/publication/PubMed/19015526" } ] } ], "crossref": [ { "id": "Q7LG56", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7LG56", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19015526", "url": "https://glygen.org/publication/PubMed/19015526", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IWKMYKQAQASFWTAEEVDL", "down_seq": "KDLPHWNKLKADEKYFISHI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13315-1", "kinase_gene_name": "ATM", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7LG56", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7LG56" }, { "database": "PubMed", "id": "19015526", "url": "https://glygen.org/publication/PubMed/19015526" } ], "site_lbl": "Ser72" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q7LG56", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q7LG56" }, { "database": "PubMed", "id": "19015526", "url": "https://glygen.org/publication/PubMed/19015526" } ], "site_lbl": "Ser72" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "323", "end_pos": "323" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "72", "end_pos": "72" } ] } ], "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P62714-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P62714-1", "length": 309, "uniprot_id": "PP2AB_HUMAN", "protein_name": "Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "refseq_ac": "NP_001009552", "refseq_name": "serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "gene_name": "PPP2CB", "gene_names_uniprotkb": "PPP2CB", "gene_names_refseq": "PP2Abeta; PP2CB; PPP2CB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Comparative O-GlcNAc Proteomic Analysis Reveals a Role of O-GlcNAcylated SAM68 in Lung Cancer Aggressiveness.", "journal": "Cancers", "date": "2022", "authors": "Lin CH, Liao CC, Wang SY, Peng CY, Yeh YC, Chen MY, Chou TY", "evidence": [ { "database": "O-GlcNAc Database", "id": "P62714", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P62714" } ], "reference": [ { "type": "PubMed", "id": "35008409", "url": "https://glygen.org/publication/PubMed/35008409" } ] }, { "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": "P62714", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P62714" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "P62714", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P62714" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "35008409", "url": "https://glygen.org/publication/PubMed/35008409", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P62714", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P62714", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "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": "35008409", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35008409" }, { "id": "P62714", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P62714" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "307", "end_pos": "307" } ] } ], "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": "P62714-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P62714-1", "length": 309, "uniprot_id": "PP2AB_HUMAN", "protein_name": "Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "refseq_ac": "NP_001009552", "refseq_name": "serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "gene_name": "PPP2CB", "gene_names_uniprotkb": "PPP2CB", "gene_names_refseq": "PP2Abeta; PP2CB; PPP2CB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A protein phosphatase methylesterase (PME-1) is one of several novel proteins stably associating with two inactive mutants of protein phosphatase 2A.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Ogris E, Du X, Nelson KC, Mak EK, Yu XX, Lane WS, Pallas DC", "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "reference": [ { "type": "PubMed", "id": "10318862", "url": "https://glygen.org/publication/PubMed/10318862" } ] } ], "crossref": [ { "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10318862", "url": "https://glygen.org/publication/PubMed/10318862", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "TLLVALKVRYPERITILRGN", "down_seq": "ESRQITQVYGFYDECLRKYG", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "Q", "comment": "Catalytically inactive. No effect on interaction with PPME1.", "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" }, { "database": "PubMed", "id": "10318862", "url": "https://glygen.org/publication/PubMed/10318862" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "307", "end_pos": "307" } ] } ], "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": "P62714-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "P62714-1", "length": 309, "uniprot_id": "PP2AB_HUMAN", "protein_name": "Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "refseq_ac": "NP_001009552", "refseq_name": "serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "gene_name": "PPP2CB", "gene_names_uniprotkb": "PPP2CB", "gene_names_refseq": "PP2Abeta; PP2CB; PPP2CB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A protein phosphatase methylesterase (PME-1) is one of several novel proteins stably associating with two inactive mutants of protein phosphatase 2A.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Ogris E, Du X, Nelson KC, Mak EK, Yu XX, Lane WS, Pallas DC", "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "reference": [ { "type": "PubMed", "id": "10318862", "url": "https://glygen.org/publication/PubMed/10318862" } ] } ], "crossref": [ { "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10318862", "url": "https://glygen.org/publication/PubMed/10318862", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LTKESNVQEVRCPVTVCGDV", "down_seq": "GQFHDLMELFRIGGKSPDTN", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "Q", "comment": "Catalytically inactive. No effect on interaction with PPME1.", "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" }, { "database": "PubMed", "id": "10318862", "url": "https://glygen.org/publication/PubMed/10318862" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "307", "end_pos": "307" } ] } ], "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": "P62714-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "P62714-1", "length": 309, "uniprot_id": "PP2AB_HUMAN", "protein_name": "Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "refseq_ac": "NP_001009552", "refseq_name": "serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "gene_name": "PPP2CB", "gene_names_uniprotkb": "PPP2CB", "gene_names_refseq": "PP2Abeta; PP2CB; PPP2CB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62714", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62714", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LQEVPHEGPMCDLLWSDPDD", "down_seq": "GGWGISPRGAGYTFGQDISE", "snv": [ { "evidence": [ { "id": "P62714", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P62714" } ], "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": "8", "chr_pos": "30794039", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R206", "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": "mutagenesis", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "307", "end_pos": "307" } ] } ], "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": "P62714-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "P62714-1", "length": 309, "uniprot_id": "PP2AB_HUMAN", "protein_name": "Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "refseq_ac": "NP_001009552", "refseq_name": "serine/threonine-protein phosphatase 2A catalytic subunit beta isoform", "gene_name": "PPP2CB", "gene_names_uniprotkb": "PPP2CB", "gene_names_refseq": "PP2Abeta; PP2CB; PPP2CB", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P62714", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P62714", "database": "PRO", "categories": [ "Other" ] }, { "id": "P62714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P62714", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LQFDPAPRRGEPHVTRRTPD", "down_seq": "FL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P62714", "url": "https://www.uniprot.org/uniprotkb/P62714" }, { "database": "PRO", "id": "P62714", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P62714" }, { "database": "iPTMnet", "id": "P62714", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P62714" } ], "site_lbl": "Tyr307" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "118", "end_pos": "118" }, { "start_pos": "59", "end_pos": "59" } ] }, { "type": "snv", "site_list": [ { "start_pos": "206", "end_pos": "206" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "307", "end_pos": "307" } ] } ], "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": "Q13123-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "KDYEETELISTTANYRAVGP", "down_seq": "AEADKSAAEKRRQLIQESKF", "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": "Thr132", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q13123-1.127.127", "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": "Q13123-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://oglcnac.org/atlas/detail/Q13123" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] }, { "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "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": "Q13123", "url": "https://oglcnac.org/atlas/detail/Q13123", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q13123", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs998430596", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs998430596", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs998430596", "url": "https://www.ensembl.org/id/rs998430596", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "QSKLTNEDFRKLLMTPRAAP", "down_seq": "SAPPSKSRHHEMPREYNEDE", "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": "Thr48", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "Q13123", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q13123" } ] } ], "snv": [ { "evidence": [ { "id": "Q13123", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123" }, { "id": "rs998430596", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs998430596" }, { "id": "rs998430596", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs998430596" } ], "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": "5", "chr_pos": "140651773", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T48", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr48" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13123-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q13123-1.49.49", "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": "Q13123-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://oglcnac.org/atlas/detail/Q13123" } ], "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": "Q13123", "url": "https://oglcnac.org/atlas/detail/Q13123", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKLTNEDFRKLLMTPRAAPT", "down_seq": "APPSKSRHHEMPREYNEDED", "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": "Ser49", "evidence": [ { "id": "31373491", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/31373491" }, { "id": "Q13123", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q13123" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q13123-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q13123-1.48.48", "categories": [ "glycosylation_flag", "snv_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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13123-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q13123", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13123" } ], "reference": [ { "type": "PubMed", "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054" } ] }, { "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": "Q13123", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13123" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q13123", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13123" } ], "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": "Q13123", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13123" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13123", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13123", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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" ] } ], "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": "34229054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34229054" }, { "id": "Q13123", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q13123" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q13123-1.6.6", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13123-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13123", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AKLRQQEIERERELAEKYRD", "down_seq": "AKERRDGVNKDYEETELIST", "snv": [ { "evidence": [ { "id": "Q13123", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123" } ], "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": "5", "chr_pos": "140653044", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R102", "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: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": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13123", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RDGVNKDYEETELISTTANY", "down_seq": "AVGPTAEADKSAAEKRRQLI", "snv": [ { "evidence": [ { "id": "Q13123", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NYR->NYS).", "chr_id": "5", "chr_pos": "140653121", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R127", "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": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q13123-1.132.132", "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": "Q13123-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs377695058", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377695058", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs377695058", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377695058#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "EELMEKPQKETKKDEDPENK", "down_seq": "EFKTRLGRNVYRMLFKSKAY", "snv": [ { "evidence": [ { "id": "rs377695058", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs377695058" }, { "id": "rs377695058", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs377695058#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKI->NKT).", "chr_id": "5", "chr_pos": "140654707", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs779907524", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779907524", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779907524", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779907524", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779907524", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779907524", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RLGRNVYRMLFKSKAYERNE", "down_seq": "FLPGRMAYVVDLDDEYADTD", "snv": [ { "evidence": [ { "id": "rs779907524", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779907524" }, { "id": "rs779907524", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779907524" }, { "id": "rs779907524", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779907524" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEL->NES).", "chr_id": "5", "chr_pos": "140655883", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L231", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13123", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "EPFSNPLAPDGHDVDDPHSF", "down_seq": "QSKLTNEDFRKLLMTPRAAP", "snv": [ { "evidence": [ { "id": "Q13123", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123" } ], "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 (HQS->NQS).", "chr_id": "5", "chr_pos": "140648533", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H27", "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": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q13123-1.42.42", "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": "Q13123-1.281.281", "start_pos": 281, "end_pos": 281, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13123", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ADCPTMEAQTTLTTNDIVIS", "down_seq": "LTQILSYLRQGTRNKKLKKK", "snv": [ { "evidence": [ { "id": "Q13123", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KLT->NLT).", "chr_id": "5", "chr_pos": "140657595", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K281", "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: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": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q13123-1.287.287", "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": "Q13123-1.319.319", "start_pos": 319, "end_pos": 319, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752550231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752550231", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752550231", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752550231", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752550231", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752550231", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "KKKDKGKLEEKKPPEADMNI", "down_seq": "EDIGDYVPSTTKTPRDKERE", "snv": [ { "evidence": [ { "id": "rs752550231", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752550231" }, { "id": "rs752550231", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752550231" }, { "id": "rs752550231", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752550231" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIF->NIS).", "chr_id": "5", "chr_pos": "140658944", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F319", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q13123-1.325.325", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q13123-1.332.332", "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": "Q13123-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q13123", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RDRDRERERERDRERERERD", "down_seq": "EREEEKKRHSYFEKPKVDDE", "snv": [ { "evidence": [ { "id": "Q13123", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q13123" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "5", "chr_pos": "140659103", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R372", "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": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.287.287", "start_pos": 287, "end_pos": 287, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EAQTTLTTNDIVISKLTQIL", "down_seq": "YLRQGTRNKKLKKKDKGKLE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "site_lbl": "Ser287" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13123-1.281.281", "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": "Q13123-1.325.325", "start_pos": 325, "end_pos": 325, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "KLEEKKPPEADMNIFEDIGD", "down_seq": "VPSTTKTPRDKERERYRERE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Tyr325" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13123-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13123-1.332.332", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q13123-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "PEADMNIFEDIGDYVPSTTK", "down_seq": "PRDKERERYRERERDRERDR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr332" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q13123-1.319.319", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q13123-1.325.325", "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": "Q13123-1.417.417", "start_pos": 417, "end_pos": 417, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "DKGPGSTKELIKSINEKFAG", "down_seq": "AGWEGTESLKKPEDKKQLGD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser417" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "DPHSFHQSKLTNEDFRKLLM", "down_seq": "PRAAPTSAPPSKSRHHEMPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr42" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q13123-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q13123-1.48.48", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q13123-1.49.49", "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": "Q13123-1.452.452", "start_pos": 452, "end_pos": 452, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "KKQLGDFFGMSNSYAECYPA", "down_seq": "MDDMAVDSDEEVDYSKMDQG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr452" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q13123-1.460.460", "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": "Q13123-1.460.460", "start_pos": 460, "end_pos": 460, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GMSNSYAECYPATMDDMAVD", "down_seq": "DEEVDYSKMDQGNKKGPLGR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser460" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q13123-1.452.452", "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": "Q13123-1.485.485", "start_pos": 485, "end_pos": 485, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ] } ], "crossref": [ { "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DYSKMDQGNKKGPLGRWDFD", "down_seq": "QEEYSEYMNNKEALPKAAFQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "18077418", "url": "https://glygen.org/publication/PubMed/18077418" } ], "site_lbl": "Thr485" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.536.536", "start_pos": 536, "end_pos": 536, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TRRFKETNDKAELDRQWKKI", "down_seq": "AIIEKRKKMEADGVEVKRPK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "site_lbl": "Ser536" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "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": "Q13123-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "Q13123-1", "length": 557, "uniprot_id": "RED_HUMAN", "protein_name": "Protein Red", "refseq_ac": "NP_006074", "refseq_name": "protein Red", "gene_name": "IK", "gene_names_uniprotkb": "IK; RED; RER", "gene_names_refseq": "CSA2; IK; RED; RER", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q13123", "url": "https://www.uniprot.org/uniprotkb/Q13123" } ], "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": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123", "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": "MPERD", "down_seq": "EPFSNPLAPDGHDVDDPHSF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q13123", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q13123" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser6" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "132", "end_pos": "132" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" } ] }, { "type": "snv", "site_list": [ { "start_pos": "102", "end_pos": "102" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "281", "end_pos": "281" }, { "start_pos": "319", "end_pos": "319" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "48", "end_pos": "48" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "287", "end_pos": "287" }, { "start_pos": "325", "end_pos": "325" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "417", "end_pos": "417" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "460", "end_pos": "460" }, { "start_pos": "485", "end_pos": "485" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "536", "end_pos": "536" }, { "start_pos": "6", "end_pos": "6" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q13123-1.0.0", "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": "P01033-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "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": "Site-specific characterization of glycoprotein carbohydrates by exoglycosidase digestion and laser desorption mass spectrometry.", "journal": "Analytical biochemistry", "date": "1994", "authors": "Sutton CW, O'Neill JA, Cottrell JS", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "reference": [ { "type": "PubMed", "id": "8053566", "url": "https://glygen.org/publication/PubMed/8053566" } ] }, { "title": "Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes.", "journal": "Journal of proteome research", "date": "2020", "authors": "Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Heck AJR", "evidence": [ { "database": "GlyConnect", "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "reference": [ { "type": "PubMed", "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "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": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "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" } ] }, { "title": "Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry.", "journal": "Journal of proteome research", "date": "2006", "authors": "Ramachandran P, Boontheung P, Xie Y, Sondej M, Wong DT, Loo JA", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "16740002", "url": "https://glygen.org/publication/PubMed/16740002" } ] }, { "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" } ] }, { "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": "8053566", "url": "https://glygen.org/publication/PubMed/8053566", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "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": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16740002", "url": "https://glygen.org/publication/PubMed/16740002", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "IRFVYTPAMESVCGYFHRSH", "down_seq": "RSEEFLIAGKLQDGLLHITT", "glycosylation": [ { "glytoucan_ac": "G01485JJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G01600VV", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G02030ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G02661MY", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G03382KH", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G05229BF", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G06356OH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G07755XJ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G08146BT", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G08290VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G10256JP", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G10944ZI", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G11314AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G11392CL", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G11870QZ", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G14994KB", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G20312EM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G20751GZ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G22310AV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G23719VF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G23863VK", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G25451PN", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G28156XV", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G29580WD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G29880MM", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G37868ZX", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G39841VH", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G41071NU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G42039DE", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G42962KI", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G44215PV", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G45495MK", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G46687AB", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G49874UX", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G51413EV", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G57081YJ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G57818FI", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G59358BQ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G61256FT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G64409MC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G66163OV", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G66504LK", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G66538GV", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G70375MX", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G71146HJ", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G71146MY", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G72667IM", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G72797UR", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G74724QE", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G75303RX", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G76295SF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G78454JO", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G79286RS", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G80333GO", "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": "Asn101", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHNRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G81263BG", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G83229XP", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G84811LS", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G86795LJ", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G89417VQ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G90093AU", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G90575OW", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G91636VS", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G92275SC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "SHnRSEEFLIAGK", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "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": "G94854LT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G96079KC", "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": "Asn101", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G96577RX", "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": "Asn101", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "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": "Asn101", "evidence": [ { "id": "P01033", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "id": "16740002", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16740002" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" } ] } ], "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [ "n-glyco-sequon-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 2 filters: n-glyco-sequon-loss (NRS->SRS); protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585305", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N101", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_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": 81 }, { "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": 80 }, { "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": 80 } ], "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": 80 }, { "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": 80 }, { "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": 80 } ], "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": 8 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P01033-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "N-Glycoproteomics of Human Seminal Plasma Glycoproteins.", "journal": "Journal of proteome research", "date": "2016", "authors": "Saraswat M, Joenvaara S, Tomar AK, Singh S, Yadav S, Renkonen R", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" } ], "reference": [ { "type": "PubMed", "id": "26791533", "url": "https://glygen.org/publication/PubMed/26791533" } ] }, { "title": "Integrated glycoproteomic characterization of clear cell renal cell carcinoma.", "journal": "Cell reports", "date": "2023-05-30", "authors": "Lih T Mamie, Cho Kyung-Cho, Schnaubelt Michael, Hu Yingwei, Zhang Hui", "evidence": [ { "database": "PDC", "id": "PDC000471", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ], "reference": [ { "type": "PubMed", "id": "37074911", "url": "https://glygen.org/publication/PubMed/37074911" } ] }, { "title": "Site-specific characterization of glycoprotein carbohydrates by exoglycosidase digestion and laser desorption mass spectrometry.", "journal": "Analytical biochemistry", "date": "1994", "authors": "Sutton CW, O'Neill JA, Cottrell JS", "evidence": [ { "database": "UniCarbKB", "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040" }, { "database": "GlyConnect", "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "reference": [ { "type": "PubMed", "id": "8053566", "url": "https://glygen.org/publication/PubMed/8053566" } ] }, { "title": "Quantitative Longitudinal Inventory of the N-Glycoproteome of Human Milk from a Single Donor Reveals the Highly Variable Repertoire and Dynamic Site-Specific Changes.", "journal": "Journal of proteome research", "date": "2020", "authors": "Zhu J, Lin YH, Dingess KA, Mank M, Stahl B, Heck AJR", "evidence": [ { "database": "GlyConnect", "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "reference": [ { "type": "PubMed", "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "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": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "reference": [ { "type": "PubMed", "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "title": "Distinct urinary glycoprotein signatures in prostate cancer patients.", "journal": "Oncotarget", "date": "2018", "authors": "Kawahara R, Ortega F, Rosa-Fernandes L, Guimaraes V, Quina D, Nahas W, Schwammle V, Srougi M, Leite KRM, Thaysen-Andersen M, Larsen MR, Palmisano G", "evidence": [ { "database": "GlyConnect", "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ], "reference": [ { "type": "PubMed", "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853" } ] }, { "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": "Human plasma N-glycoproteome analysis by immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry.", "journal": "Journal of proteome research", "date": "2005", "authors": "Liu T, Qian WJ, Gritsenko MA, Camp DG 2nd, Monroe ME, Moore RJ, Smith RD", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952" } ] }, { "title": "Identification of N-linked glycoproteins in human saliva by glycoprotein capture and mass spectrometry.", "journal": "Journal of proteome research", "date": "2006", "authors": "Ramachandran P, Boontheung P, Xie Y, Sondej M, Wong DT, Loo JA", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "16740002", "url": "https://glygen.org/publication/PubMed/16740002" } ] }, { "title": "A strategy for precise and large scale identification of core fucosylated glycoproteins.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Jia W, Lu Z, Fu Y, Wang HP, Wang LH, Chi H, Yuan ZF, Zheng ZB, Song LN, Han HH, Liang YM, Wang JL, Cai Y, Zhang YK, Deng YL, Ying WT, He SM, Qian XH", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "19139490", "url": "https://glygen.org/publication/PubMed/19139490" } ] }, { "title": "Elucidation of N-glycosylation sites on human platelet proteins: a glycoproteomic approach.", "journal": "Molecular & cellular proteomics : MCP", "date": "2006", "authors": "Lewandrowski U, Moebius J, Walter U, Sickmann A", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "16263699", "url": "https://glygen.org/publication/PubMed/16263699" } ] }, { "title": "Quantification of the N-glycosylated secretome by super-SILAC during breast cancer progression and in human blood samples.", "journal": "Molecular & cellular proteomics : MCP", "date": "2013", "authors": "Boersema PJ, Geiger T, Wisniewski JR, Mann M", "evidence": [ { "database": "GlyGen", "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143" } ], "reference": [ { "type": "PubMed", "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970" } ] }, { "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": "26791533", "url": "https://glygen.org/publication/PubMed/26791533", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000040", "url": "http://data.glygen.org/GLY_000040", "database": "UniCarbKB", "categories": [] }, { "id": "P01033@N53", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53", "database": "GPTwiki", "categories": [ "Other" ] }, { "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": "8053566", "url": "https://glygen.org/publication/PubMed/8053566", "database": "PubMed", "categories": [ "Other" ] }, { "id": "367", "url": "https://glyconnect.expasy.org/browser/proteins/367", "database": "GlyConnect", "categories": [ "Glycomics", "Glycoproteomics" ] }, { "id": "32125861", "url": "https://glygen.org/publication/PubMed/32125861", "database": "PubMed", "categories": [ "Other" ] }, { "id": "29741879", "url": "https://glygen.org/publication/PubMed/29741879", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30237853", "url": "https://glygen.org/publication/PubMed/30237853", "database": "PubMed", "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": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16335952", "url": "https://glygen.org/publication/PubMed/16335952", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16740002", "url": "https://glygen.org/publication/PubMed/16740002", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19139490", "url": "https://glygen.org/publication/PubMed/19139490", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16263699", "url": "https://glygen.org/publication/PubMed/16263699", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23090970", "url": "https://glygen.org/publication/PubMed/23090970", "database": "PubMed", "categories": [ "Other" ] }, { "id": "GLY_000143", "url": "https://data.glygen.org/GLY_000143", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "24190977", "url": "https://glygen.org/publication/PubMed/24190977", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TAFCNSDLVIRAKFVGTPEV", "down_seq": "QTTLYQRYEIKMTKMYKGFQ", "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": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" }, { "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": "G01600VV", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G02030ZB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G02528FI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G02661MY", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G02815KT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G03382KH", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G04657PL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G05049YU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G05229BF", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G08146BT", "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": "Asn53", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G08290VR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G08918WF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G10256JP", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G10339FR", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G10819WX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G10944ZI", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G11314AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G11392CL", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G11629QQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G11870QZ", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G11911BT", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G12580WI", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "glytoucan_ac": "G14972EH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G14994KB", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G15169WU", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G19379ID", "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": "Asn53", "evidence": [ { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "glytoucan_ac": "G20751GZ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G22310AV", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "30237853", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30237853" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G23719VF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G23863VK", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G24202BK", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G25713RA", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G26271XI", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G27058EU", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G28156XV", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G29880MM", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G31483BB", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G31852PQ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G34989PA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G35253PZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G39841VH", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G40834TG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G41126SR", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G41247ZX", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G42039DE", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G42124LM", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G43223CG", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G43734MM", "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": "Asn53", "evidence": [ { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "glytoucan_ac": "G44953PJ", "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": "Asn53", "evidence": [ { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "glytoucan_ac": "G45395BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G45495MK", "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": "Asn53", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G46687AB", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G46691LC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G47644PP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G47950XN", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G49874UX", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G51413EV", "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": "Asn53", "evidence": [ { "id": "30237853", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30237853" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G56284ZY", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G57081YJ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G57776ZS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G59358BQ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G59626AS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G60923RB", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G62765YT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVNQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G64409MC", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G66504LK", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G68318VE", "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": "Asn53", "evidence": [ { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "glytoucan_ac": "G69521XL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G70087PV", "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": "Asn53", "evidence": [ { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G70232NH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G70375MX", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G70441OD", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G70822IO", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G71146HJ", "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": "Asn53", "evidence": [ { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G71146MY", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G72667IM", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G72797UR", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" } ] }, { "glytoucan_ac": "G74724QE", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G75303RX", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G75607BQ", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G75983OB", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G76295SF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G77122IZ", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G78454JO", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G79666IR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "37074911", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37074911" }, { "id": "PDC000471", "database": "PDC", "url": "https://proteomic.datacommons.cancer.gov/pdc/study/PDC000471" } ] }, { "glytoucan_ac": "G80075MS", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G80333GO", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G80920RR", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G81198YO", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G81263BG", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G82592ZH", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G83460ZZ", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G83555HU", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G83633GK", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" }, { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "32125861", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32125861" } ] }, { "glytoucan_ac": "G84811LS", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G86880BF", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G87051GH", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G88374WZ", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "P01033@N53", "database": "GPTwiki", "url": "https://edwardslab.bmcb.georgetown.edu/gptwiki/P01033@N53" } ] }, { "glytoucan_ac": "G89417VQ", "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": "GlycoSuiteDB curation notes. Reported structure can be attached to the following: N-53, N-101", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G90093AU", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G90382BL", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G91636VS", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G92135MA", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G94854LT", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "N", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G95177YH", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "FVGTPEVnQTTLYQR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "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": "G95835XS", "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": "Asn53", "evidence": [ { "id": "26791533", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/26791533" }, { "id": "GLY_000040", "database": "UniCarbKB", "url": "http://data.glygen.org/GLY_000040" } ] }, { "glytoucan_ac": "G95977AE", "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": "Asn53", "evidence": [ { "id": "29741879", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29741879" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "G96079KC", "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": "Asn53", "evidence": [ { "id": "8053566", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/8053566" }, { "id": "367", "database": "GlyConnect", "url": "https://glyconnect.expasy.org/browser/proteins/367" } ] }, { "glytoucan_ac": "", "type": "N-linked", "subtype": "Complex", "prediction_tool_list": [], "site_category": "reported", "site_category_dict": { "reported": true }, "site_seq": "N", "relation": "attached", "comment": "N-linked (GlcNAc...) (complex) asparagine;Complex", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn53", "evidence": [ { "id": "P01033", "database": "UniProtKB", "url": "https://www.uniprot.org/uniprotkb/P01033#ptm_processing" }, { "id": "16335952", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16335952" }, { "id": "16740002", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16740002" }, { "id": "19139490", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/19139490" }, { "id": "16263699", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/16263699" }, { "id": "23090970", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23090970" }, { "id": "GLY_000143", "database": "GlyGen", "url": "https://data.glygen.org/GLY_000143" }, { "id": "24190977", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/24190977" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.73.73", "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": 118 }, { "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": 117 }, { "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": 117 } ], "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": 117 }, { "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": 117 }, { "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": 117 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 13 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P01033-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "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": "P01033", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P01033" } ], "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": "P01033", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P01033", "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": "P01033", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P01033" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P01033-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The intrinsic protein flexibility of endogenous protease inhibitor TIMP-1 controls its binding interface and affects its function.", "journal": "Biochemistry", "date": "2010", "authors": "Grossman M, Tworowski D, Dym O, Lee MH, Levy Y, Murphy G, Sagi I", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "20545310", "url": "https://glygen.org/publication/PubMed/20545310" } ] } ], "crossref": [ { "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20545310", "url": "https://glygen.org/publication/PubMed/20545310", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1387551262", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1387551262", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1387551262", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1387551262", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NRSEEFLIAGKLQDGLLHIT", "down_seq": "CSFVAPWNSLSLAQRRGFTK", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "L", "comment": "Decreases protein flexibility and increases affinity for MMP14.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "20545310", "url": "https://glygen.org/publication/PubMed/20545310" } ] } ], "snv": [ { "evidence": [ { "id": "rs1387551262", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1387551262" }, { "id": "rs1387551262", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1387551262" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585575", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T121", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.141.141", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P01033-1.25.25", "start_pos": 25, "end_pos": 25, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Crystal structure of the catalytic domain of matrix metalloproteinase-1 in complex with the inhibitory domain of tissue inhibitor of metalloproteinase-1.", "journal": "The Journal of biological chemistry", "date": "2007", "authors": "Iyer S, Wei S, Brew K, Acharya KR", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] } ], "crossref": [ { "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EPLASGILLLLWLIAPSRAC", "down_seq": "CVPPHPQTAFCNSDLVIRAK", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "E", "comment": "Reduced interaction with metalloproteinase.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] }, { "sequence_org": "T", "sequence_mut": "G", "comment": "Reduced interaction with metalloproteinase.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] }, { "sequence_org": "T", "sequence_mut": "K", "comment": "Reduced interaction with metalloproteinase.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] }, { "sequence_org": "T", "sequence_mut": "Q", "comment": "Reduced interaction with metalloproteinase.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] }, { "sequence_org": "T", "sequence_mut": "R", "comment": "Reduced interaction with metalloproteinase.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] }, { "sequence_org": "T", "sequence_mut": "V", "comment": "Normal interaction with metalloproteinase.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "17050530", "url": "https://glygen.org/publication/PubMed/17050530" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.44.44", "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": "P01033-1.30.30", "start_pos": 30, "end_pos": 30, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Metalloproteinase inhibition and erythroid potentiation are independent activities of tissue inhibitor of metalloproteinases-1.", "journal": "Blood", "date": "1995", "authors": "Chesler L, Golde DW, Bersch N, Johnson MD", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "8541540", "url": "https://glygen.org/publication/PubMed/8541540" } ] } ], "crossref": [ { "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8541540", "url": "https://glygen.org/publication/PubMed/8541540", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "GILLLLWLIAPSRACTCVPP", "down_seq": "PQTAFCNSDLVIRAKFVGTP", "mutagenesis": [ { "sequence_org": "H", "sequence_mut": "A", "comment": "Nearly abolishes metalloproteinase inhibition.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "8541540", "url": "https://glygen.org/publication/PubMed/8541540" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.50.50", "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": "P01033-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Metalloproteinase inhibition and erythroid potentiation are independent activities of tissue inhibitor of metalloproteinases-1.", "journal": "Blood", "date": "1995", "authors": "Chesler L, Golde DW, Bersch N, Johnson MD", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "reference": [ { "type": "PubMed", "id": "8541540", "url": "https://glygen.org/publication/PubMed/8541540" } ] } ], "crossref": [ { "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "8541540", "url": "https://glygen.org/publication/PubMed/8541540", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs1033715412", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033715412", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1033715412", "url": "https://www.ensembl.org/id/rs1033715412", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LLLLWLIAPSRACTCVPPHP", "down_seq": "TAFCNSDLVIRAKFVGTPEV", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Nearly abolishes metalloproteinase inhibition.", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "PubMed", "id": "8541540", "url": "https://glygen.org/publication/PubMed/8541540" } ] } ], "snv": [ { "evidence": [ { "id": "rs1033715412", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033715412" }, { "id": "rs1033715412", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1033715412" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583510", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q32", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.52.52", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "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": "P01033-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs754631765", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754631765", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs754631765", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754631765", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs754631765", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754631765", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs754631765", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754631765#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs754631765", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754631765", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs754631765", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754631765", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs140600134", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140600134", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs140600134", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140600134", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs140600134", "url": "https://www.ncbi.nlm.nih.gov/snp/rs140600134#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs140600134", "url": "http://gnomad.broadinstitute.org/awesome?query=rs140600134", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RFVYTPAMESVCGYFHRSHN", "down_seq": "SEEFLIAGKLQDGLLHITTC", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs754631765", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754631765" }, { "id": "rs754631765", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754631765" }, { "id": "rs754631765", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs754631765" }, { "id": "rs754631765", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs754631765#frequency_tab" }, { "id": "rs754631765", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs754631765" }, { "id": "rs754631765", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs754631765" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585307", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R102", "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:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs140600134", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140600134" }, { "id": "rs140600134", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs140600134" }, { "id": "rs140600134", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs140600134#frequency_tab" }, { "id": "rs140600134", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs140600134" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585308", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R102", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585308", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R102", "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": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.121.121", "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": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.171.171", "start_pos": 171, "end_pos": 171, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs199775125", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199775125", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199775125", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199775125", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199775125", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199775125", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199775125", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199775125#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199775125", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199775125", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199775125", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199775125", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1245742011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245742011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245742011", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1245742011#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TVFPCLSIPCKLQSGTHCLW", "down_seq": "DQLLQGSEKGFQSRHLACLP", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs199775125", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199775125" }, { "id": "rs199775125", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199775125" }, { "id": "rs199775125", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199775125" }, { "id": "rs199775125", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199775125#frequency_tab" }, { "id": "rs199775125", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199775125" }, { "id": "rs199775125", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199775125" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 2 filters: num. of cancers (4); protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586579", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T171", "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: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: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" ] }, { "evidence": [ { "id": "rs1245742011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245742011" }, { "id": "rs1245742011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1245742011#frequency_tab" } ], "glycoeffect": [], "sequence_org": "T", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586578", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T171", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.100.100", "start_pos": 100, "end_pos": 100, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2147918811", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147918811", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147918811", "url": "https://www.ensembl.org/id/rs2147918811", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DIRFVYTPAMESVCGYFHRS", "down_seq": "NRSEEFLIAGKLQDGLLHIT", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585301", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H100", "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": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs2147918811", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147918811" }, { "id": "rs2147918811", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147918811" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585303", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H100", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.118.118", "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": 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": "P01033-1.104.104", "start_pos": 104, "end_pos": 104, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1203645563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203645563", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1203645563", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203645563", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "VYTPAMESVCGYFHRSHNRS", "down_seq": "EFLIAGKLQDGLLHITTCSF", "snv": [ { "evidence": [ { "id": "rs1203645563", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203645563" }, { "id": "rs1203645563", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203645563" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585313", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E104", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.124.124", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.105.105", "start_pos": 105, "end_pos": 105, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778571038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778571038", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778571038", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs778571038", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs778571038", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778571038", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778571038", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778571038#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778571038", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778571038", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YTPAMESVCGYFHRSHNRSE", "down_seq": "FLIAGKLQDGLLHITTCSFV", "snv": [ { "evidence": [ { "id": "rs778571038", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778571038" }, { "id": "rs778571038", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs778571038" }, { "id": "rs778571038", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778571038" }, { "id": "rs778571038", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs778571038#frequency_tab" }, { "id": "rs778571038", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778571038" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585317", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E105", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1199287782", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1199287782", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1199287782", "url": "https://www.ensembl.org/id/rs1199287782", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "TPAMESVCGYFHRSHNRSEE", "down_seq": "LIAGKLQDGLLHITTCSFVA", "snv": [ { "evidence": [ { "id": "rs1199287782", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1199287782" }, { "id": "rs1199287782", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1199287782" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585319", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "PAMESVCGYFHRSHNRSEEF", "down_seq": "IAGKLQDGLLHITTCSFVAP", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585322", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L107", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs886136735", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886136735", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs886136735", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886136735#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs778604145", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778604145", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778604145", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778604145", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778604145", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778604145", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "AMESVCGYFHRSHNRSEEFL", "down_seq": "AGKLQDGLLHITTCSFVAPW", "snv": [ { "evidence": [ { "id": "rs886136735", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs886136735" }, { "id": "rs886136735", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs886136735#frequency_tab" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585325", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I108", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs778604145", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778604145" }, { "id": "rs778604145", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778604145" }, { "id": "rs778604145", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778604145" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585327", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I108", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769627219", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769627219", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769627219", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769627219", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs769627219", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769627219", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769627219", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769627219", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2057808518", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808518", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057808518", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057808518#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MAPFEPLAS", "down_seq": "ILLLLWLIAPSRACTCVPPH", "snv": [ { "evidence": [ { "id": "rs769627219", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769627219" }, { "id": "rs769627219", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769627219" }, { "id": "rs769627219", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769627219" }, { "id": "rs769627219", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769627219" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583444", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G10", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2057808518", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808518" }, { "id": "rs2057808518", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057808518#frequency_tab" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583443", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G10", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057820836", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057820836", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057820836", "url": "https://www.ensembl.org/id/rs2057820836", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ESVCGYFHRSHNRSEEFLIA", "down_seq": "KLQDGLLHITTCSFVAPWNS", "snv": [ { "evidence": [ { "id": "rs2057820836", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057820836" }, { "id": "rs2057820836", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057820836" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585543", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G110", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1171246821", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171246821", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1171246821", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171246821", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "CGYFHRSHNRSEEFLIAGKL", "down_seq": "DGLLHITTCSFVAPWNSLSL", "snv": [ { "evidence": [ { "id": "rs1171246821", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171246821" }, { "id": "rs1171246821", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171246821" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585553", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q113", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs765441951", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765441951", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765441951", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765441951", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765441951", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765441951", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GYFHRSHNRSEEFLIAGKLQ", "down_seq": "GLLHITTCSFVAPWNSLSLA", "snv": [ { "evidence": [ { "id": "rs765441951", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765441951" }, { "id": "rs765441951", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765441951" }, { "id": "rs765441951", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765441951" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585554", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D114", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.134.134", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1457756073", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457756073", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1457756073", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1457756073#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1457756073", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1457756073", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YFHRSHNRSEEFLIAGKLQD", "down_seq": "LLHITTCSFVAPWNSLSLAQ", "snv": [ { "evidence": [ { "id": "rs1457756073", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1457756073" }, { "id": "rs1457756073", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1457756073#frequency_tab" }, { "id": "rs1457756073", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1457756073" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585557", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G115", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.118.118", "start_pos": 118, "end_pos": 118, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "RSHNRSEEFLIAGKLQDGLL", "down_seq": "ITTCSFVAPWNSLSLAQRRG", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585566", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H118", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057821046", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057821046", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057821046", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2057821046", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SEEFLIAGKLQDGLLHITTC", "down_seq": "FVAPWNSLSLAQRRGFTKTY", "snv": [ { "evidence": [ { "id": "rs2057821046", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057821046" }, { "id": "rs2057821046", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2057821046" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585582", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S123", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs4898", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4898", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs4898", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4898", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs4898", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4898", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs4898", "url": "https://www.ncbi.nlm.nih.gov/snp/rs4898#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs4898", "url": "http://gnomad.broadinstitute.org/awesome?query=rs4898", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "EEFLIAGKLQDGLLHITTCS", "down_seq": "VAPWNSLSLAQRRGFTKTYT", "snv": [ { "evidence": [ { "id": "rs4898", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4898" }, { "id": "rs4898", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs4898" }, { "id": "rs4898", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs4898" }, { "id": "rs4898", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs4898#frequency_tab" }, { "id": "rs4898", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs4898" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585586", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F124", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1238291034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238291034", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1238291034", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1238291034#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "EFLIAGKLQDGLLHITTCSF", "down_seq": "APWNSLSLAQRRGFTKTYTV", "snv": [ { "evidence": [ { "id": "rs1238291034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1238291034" }, { "id": "rs1238291034", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1238291034#frequency_tab" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585587", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V125", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769442128", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769442128", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769442128", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769442128", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769442128", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769442128#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769442128", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769442128", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1396542894", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1396542894", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1396542894", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1396542894#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1396542894", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1396542894", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1396542894", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1396542894", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1324693482", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324693482", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1324693482", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1324693482#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1324693482", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324693482", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FLIAGKLQDGLLHITTCSFV", "down_seq": "PWNSLSLAQRRGFTKTYTVG", "snv": [ { "evidence": [ { "id": "rs769442128", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769442128" }, { "id": "rs769442128", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769442128" }, { "id": "rs769442128", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769442128#frequency_tab" }, { "id": "rs769442128", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769442128" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585379", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A126", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1396542894", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1396542894" }, { "id": "rs1396542894", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1396542894#frequency_tab" }, { "id": "rs1396542894", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1396542894" }, { "id": "rs1396542894", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1396542894" }, { "id": "rs1324693482", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324693482" }, { "id": "rs1324693482", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1324693482#frequency_tab" }, { "id": "rs1324693482", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324693482" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585380", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A126", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.127.127", "start_pos": 127, "end_pos": 127, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs967290911", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs967290911", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs967290911", "url": "https://www.ncbi.nlm.nih.gov/snp/rs967290911#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs967290911", "url": "http://gnomad.broadinstitute.org/awesome?query=rs967290911", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LIAGKLQDGLLHITTCSFVA", "down_seq": "WNSLSLAQRRGFTKTYTVGC", "snv": [ { "evidence": [ { "id": "rs967290911", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs967290911" }, { "id": "rs967290911", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs967290911#frequency_tab" }, { "id": "rs967290911", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs967290911" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585594", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P127", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs967290911", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs967290911" }, { "id": "rs967290911", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs967290911#frequency_tab" }, { "id": "rs967290911", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs967290911" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585594", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P127", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.128.128", "start_pos": 128, "end_pos": 128, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057821196", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057821196", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057821196", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2057821196", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs779789635", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779789635", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779789635", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779789635", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779789635", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs779789635", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs779789635", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779789635", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "IAGKLQDGLLHITTCSFVAP", "down_seq": "NSLSLAQRRGFTKTYTVGCE", "snv": [ { "evidence": [ { "id": "rs2057821196", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057821196" }, { "id": "rs2057821196", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2057821196" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585597", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W128", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs779789635", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779789635" }, { "id": "rs779789635", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779789635" }, { "id": "rs779789635", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs779789635" }, { "id": "rs779789635", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779789635" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "NC_000023.11", "chr_pos": "47585596", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "W128", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs751311919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751311919", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs751311919", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751311919", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs751311919", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751311919#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs751311919", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751311919", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKLQDGLLHITTCSFVAPWN", "down_seq": "LSLAQRRGFTKTYTVGCEEC", "snv": [ { "evidence": [ { "id": "rs751311919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751311919" }, { "id": "rs751311919", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751311919" }, { "id": "rs751311919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751311919#frequency_tab" }, { "id": "rs751311919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751311919" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585602", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S130", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585603", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S130", "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": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs751311919", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751311919" }, { "id": "rs751311919", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs751311919" }, { "id": "rs751311919", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs751311919#frequency_tab" }, { "id": "rs751311919", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs751311919" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585604", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "S130", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "subjects_tested", "subjects_positive", "frequency" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.132.132", "start_pos": 132, "end_pos": 132, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs781122069", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781122069", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs781122069", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781122069", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs781122069", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781122069#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs781122069", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781122069", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LQDGLLHITTCSFVAPWNSL", "down_seq": "LAQRRGFTKTYTVGCEECTV", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs781122069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781122069" }, { "id": "rs781122069", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781122069" }, { "id": "rs781122069", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781122069#frequency_tab" }, { "id": "rs781122069", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781122069" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585609", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S132", "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": "rs781122069", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781122069" }, { "id": "rs781122069", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs781122069" }, { "id": "rs781122069", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs781122069#frequency_tab" }, { "id": "rs781122069", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs781122069" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585609", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S132", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "P01033-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1478486447", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1478486447", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1478486447", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1478486447", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1172953948", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172953948", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1172953948", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1172953948#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1172953948", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172953948", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs764050293", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764050293", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764050293", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764050293", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764050293", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764050293", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DGLLHITTCSFVAPWNSLSL", "down_seq": "QRRGFTKTYTVGCEECTVFP", "snv": [ { "evidence": [ { "id": "rs1478486447", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1478486447" }, { "id": "rs1478486447", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1478486447" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585615", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A134", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1172953948", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172953948" }, { "id": "rs1172953948", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1172953948#frequency_tab" }, { "id": "rs1172953948", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172953948" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585403", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A134", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1172953948", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1172953948" }, { "id": "rs1172953948", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1172953948#frequency_tab" }, { "id": "rs1172953948", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1172953948" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585403", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A134", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs764050293", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764050293" }, { "id": "rs764050293", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764050293" }, { "id": "rs764050293", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764050293" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585404", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A134", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.154.154", "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": 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": "P01033-1.135.135", "start_pos": 135, "end_pos": 135, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1417127009", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417127009", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1417127009", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1417127009", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "GLLHITTCSFVAPWNSLSLA", "down_seq": "RRGFTKTYTVGCEECTVFPC", "snv": [ { "evidence": [ { "id": "rs1417127009", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1417127009" }, { "id": "rs1417127009", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1417127009" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585618", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q135", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.154.154", "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": "P01033-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1474181557", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474181557", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1474181557", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1474181557#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1474181557", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474181557", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199939406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199939406", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs199939406", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199939406", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs199939406", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199939406", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs199939406", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199939406#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs199939406", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199939406", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs199939406", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199939406", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLHITTCSFVAPWNSLSLAQ", "down_seq": "RGFTKTYTVGCEECTVFPCL", "snv": [ { "evidence": [ { "id": "rs1474181557", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1474181557" }, { "id": "rs1474181557", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1474181557#frequency_tab" }, { "id": "rs1474181557", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1474181557" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585620", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R136", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs199939406", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199939406" }, { "id": "rs199939406", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199939406" }, { "id": "rs199939406", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs199939406" }, { "id": "rs199939406", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs199939406#frequency_tab" }, { "id": "rs199939406", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs199939406" }, { "id": "rs199939406", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs199939406" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585621", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R136", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P01033-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777619063", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777619063", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777619063", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777619063", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777619063", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777619063#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs777619063", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777619063", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LHITTCSFVAPWNSLSLAQR", "down_seq": "GFTKTYTVGCEECTVFPCLS", "snv": [ { "evidence": [ { "id": "rs777619063", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777619063" }, { "id": "rs777619063", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777619063" }, { "id": "rs777619063", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs777619063#frequency_tab" }, { "id": "rs777619063", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777619063" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585624", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R137", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585623", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R137", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.138.138", "start_pos": 138, "end_pos": 138, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1284941999", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284941999", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1284941999", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284941999", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "HITTCSFVAPWNSLSLAQRR", "down_seq": "FTKTYTVGCEECTVFPCLSI", "snv": [ { "evidence": [ { "id": "rs1284941999", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1284941999" }, { "id": "rs1284941999", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1284941999" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585627", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G138", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.118.118", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1401979268", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1401979268", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1401979268", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1401979268", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TTCSFVAPWNSLSLAQRRGF", "down_seq": "KTYTVGCEECTVFPCLSIPC", "snv": [ { "evidence": [ { "id": "rs1401979268", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1401979268" }, { "id": "rs1401979268", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1401979268" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585633", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T140", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.141.141", "start_pos": 141, "end_pos": 141, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1278889417", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1278889417", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1278889417", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1278889417", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1278889417", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1278889417", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "TCSFVAPWNSLSLAQRRGFT", "down_seq": "TYTVGCEECTVFPCLSIPCK", "snv": [ { "evidence": [ { "id": "rs1278889417", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1278889417" }, { "id": "rs1278889417", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1278889417" }, { "id": "rs1278889417", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1278889417" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585635", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K141", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.121.121", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1355460480", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355460480", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1355460480", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355460480", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "CSFVAPWNSLSLAQRRGFTK", "down_seq": "YTVGCEECTVFPCLSIPCKL", "snv": [ { "evidence": [ { "id": "rs1355460480", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355460480" }, { "id": "rs1355460480", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355460480" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585639", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T142", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.123.123", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.144.144", "start_pos": 144, "end_pos": 144, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770667933", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770667933", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770667933", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770667933", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770667933", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770667933", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1449836847", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1449836847", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1449836847", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1449836847#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1449836847", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1449836847", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FVAPWNSLSLAQRRGFTKTY", "down_seq": "VGCEECTVFPCLSIPCKLQS", "snv": [ { "evidence": [ { "id": "rs770667933", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770667933" }, { "id": "rs770667933", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770667933" }, { "id": "rs770667933", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770667933" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585644", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T144", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1449836847", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1449836847" }, { "id": "rs1449836847", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1449836847#frequency_tab" }, { "id": "rs1449836847", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1449836847" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585645", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T144", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P01033-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VAPWNSLSLAQRRGFTKTYT", "down_seq": "GCEECTVFPCLSIPCKLQSG", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585648", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "V145", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.125.125", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.127.127", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.148.148", "start_pos": 148, "end_pos": 148, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2057821851", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057821851", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057821851", "url": "https://www.ensembl.org/id/rs2057821851", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "WNSLSLAQRRGFTKTYTVGC", "down_seq": "ECTVFPCLSIPCKLQSGTHC", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs2057821851", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057821851" }, { "id": "rs2057821851", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057821851" } ], "glycoeffect": [], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585658", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E148", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.128.128", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.151.151", "start_pos": 151, "end_pos": 151, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1603059315", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1603059315", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1603059315", "url": "https://www.ensembl.org/id/rs1603059315", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LSLAQRRGFTKTYTVGCEEC", "down_seq": "VFPCLSIPCKLQSGTHCLWT", "snv": [ { "evidence": [ { "id": "rs1603059315", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1603059315" }, { "id": "rs1603059315", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1603059315" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585666", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T151", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.171.171", "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": "P01033-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1426472242", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426472242", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1426472242", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426472242", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SLAQRRGFTKTYTVGCEECT", "down_seq": "FPCLSIPCKLQSGTHCLWTD", "snv": [ { "evidence": [ { "id": "rs1426472242", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1426472242" }, { "id": "rs1426472242", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1426472242" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586521", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V152", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.132.132", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "LAQRRGFTKTYTVGCEECTV", "down_seq": "PCLSIPCKLQSGTHCLWTDQ", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586525", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "F153", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.154.154", "start_pos": 154, "end_pos": 154, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "AQRRGFTKTYTVGCEECTVF", "down_seq": "CLSIPCKLQSGTHCLWTDQL", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586528", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P154", "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": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586527", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P154", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.134.134", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.135.135", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P01033-1.156.156", "start_pos": 156, "end_pos": 156, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs767313689", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767313689", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs767313689", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767313689", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs767313689", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767313689#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs767313689", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767313689", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "RRGFTKTYTVGCEECTVFPC", "down_seq": "SIPCKLQSGTHCLWTDQLLQ", "snv": [ { "evidence": [ { "id": "rs767313689", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767313689" }, { "id": "rs767313689", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs767313689" }, { "id": "rs767313689", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs767313689#frequency_tab" }, { "id": "rs767313689", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs767313689" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586533", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L156", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.136.136", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.157.157", "start_pos": 157, "end_pos": 157, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RGFTKTYTVGCEECTVFPCL", "down_seq": "IPCKLQSGTHCLWTDQLLQG", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586537", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S157", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.138.138", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.159.159", "start_pos": 159, "end_pos": 159, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1245605085", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245605085", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1245605085", "url": "https://www.ensembl.org/id/rs1245605085", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1245605085", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1245605085", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "FTKTYTVGCEECTVFPCLSI", "down_seq": "CKLQSGTHCLWTDQLLQGSE", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1245605085", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1245605085" }, { "id": "rs1245605085", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1245605085" }, { "id": "rs1245605085", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1245605085" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586543", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P159", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.160.160", "start_pos": 160, "end_pos": 160, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1388939513", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1388939513", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1388939513", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1388939513", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "TKTYTVGCEECTVFPCLSIP", "down_seq": "KLQSGTHCLWTDQLLQGSEK", "snv": [ { "evidence": [ { "id": "rs1388939513", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1388939513" }, { "id": "rs1388939513", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1388939513" } ], "glycoeffect": [], "sequence_org": "C", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586545", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "C160", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586546", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "C160", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.140.140", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.141.141", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "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": "P01033-1.162.162", "start_pos": 162, "end_pos": 162, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs756099659", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756099659", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs756099659", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756099659", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs756099659", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756099659#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs756099659", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756099659", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TYTVGCEECTVFPCLSIPCK", "down_seq": "QSGTHCLWTDQLLQGSEKGF", "snv": [ { "evidence": [ { "id": "rs756099659", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756099659" }, { "id": "rs756099659", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs756099659" }, { "id": "rs756099659", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs756099659#frequency_tab" }, { "id": "rs756099659", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs756099659" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586551", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L162", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.142.142", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.144.144", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.167.167", "start_pos": 167, "end_pos": 167, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs764066211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764066211", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs764066211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764066211", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs764066211", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764066211", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "CEECTVFPCLSIPCKLQSGT", "down_seq": "CLWTDQLLQGSEKGFQSRHL", "snv": [ { "evidence": [ { "id": "rs764066211", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764066211" }, { "id": "rs764066211", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs764066211" }, { "id": "rs764066211", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs764066211" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586568", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H167", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.148.148", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.16.16", "start_pos": 16, "end_pos": 16, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs980389577", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs980389577", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs980389577", "url": "https://www.ensembl.org/id/rs980389577", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "MAPFEPLASGILLLL", "down_seq": "LIAPSRACTCVPPHPQTAFC", "snv": [ { "evidence": [ { "id": "rs980389577", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs980389577" }, { "id": "rs980389577", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs980389577" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583463", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W16", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.33.33", "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": "P01033-1.170.170", "start_pos": 170, "end_pos": 170, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs17850165", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17850165", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs17850165", "url": "https://www.ensembl.org/id/rs17850165", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs374544466", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374544466", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs374544466", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374544466#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs374544466", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374544466", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "CTVFPCLSIPCKLQSGTHCL", "down_seq": "TDQLLQGSEKGFQSRHLACL", "snv": [ { "evidence": [ { "id": "rs17850165", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs17850165" }, { "id": "rs17850165", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs17850165" }, { "id": "rs374544466", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs374544466" }, { "id": "rs374544466", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs374544466#frequency_tab" }, { "id": "rs374544466", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs374544466" } ], "glycoeffect": [], "sequence_org": "W", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586577", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W170", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.151.151", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057827944", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057827944", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057827944", "url": "https://www.ensembl.org/id/rs2057827944", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs745510633", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745510633", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745510633", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745510633", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745510633", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745510633#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745510633", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745510633", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VFPCLSIPCKLQSGTHCLWT", "down_seq": "QLLQGSEKGFQSRHLACLPR", "snv": [ { "evidence": [ { "id": "rs2057827944", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057827944" }, { "id": "rs2057827944", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057827944" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586582", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D172", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs745510633", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745510633" }, { "id": "rs745510633", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745510633" }, { "id": "rs745510633", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745510633#frequency_tab" }, { "id": "rs745510633", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745510633" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586583", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D172", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.153.153", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.154.154", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P01033-1.176.176", "start_pos": 176, "end_pos": 176, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057828045", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828045", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057828045", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057828045#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LSIPCKLQSGTHCLWTDQLL", "down_seq": "GSEKGFQSRHLACLPREPGL", "snv": [ { "evidence": [ { "id": "rs2057828045", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828045" }, { "id": "rs2057828045", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057828045#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586594", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q176", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.156.156", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.157.157", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.195.195", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.178.178", "start_pos": 178, "end_pos": 178, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "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": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "Reactome", "id": "R-HSA-381426", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-381426" }, { "database": "iPTMnet", "id": "P01033", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P01033" } ], "reference": [ { "type": "PubMed", "id": "26091039", "url": "https://glygen.org/publication/PubMed/26091039" } ] } ], "crossref": [ { "id": "rs2057828065", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828065", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057828065", "url": "https://www.ensembl.org/id/rs2057828065", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1062849", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1062849", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1062849", "url": "https://www.ensembl.org/id/rs1062849", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P01033", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P01033", "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": "IPCKLQSGTHCLWTDQLLQG", "down_seq": "EKGFQSRHLACLPREPGLCT", "snv": [ { "evidence": [ { "id": "rs2057828065", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828065" }, { "id": "rs2057828065", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057828065" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586599", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S178", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1062849", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1062849" }, { "id": "rs1062849", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1062849" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586600", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S178", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by FAM20C", "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" }, { "database": "iPTMnet", "id": "P01033", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P01033" }, { "database": "PubMed", "id": "26091039", "url": "https://glygen.org/publication/PubMed/26091039" } ], "site_lbl": "Ser178" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": true, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "P01033-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057828113", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828113", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057828113", "url": "https://www.ensembl.org/id/rs2057828113", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PCKLQSGTHCLWTDQLLQGS", "down_seq": "KGFQSRHLACLPREPGLCTW", "snv": [ { "evidence": [ { "id": "rs2057828113", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828113" }, { "id": "rs2057828113", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057828113" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586603", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E179", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.159.159", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.195.195", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.180.180", "start_pos": 180, "end_pos": 180, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "CKLQSGTHCLWTDQLLQGSE", "down_seq": "GFQSRHLACLPREPGLCTWQ", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586607", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K180", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.160.160", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.200.200", "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": "P01033-1.181.181", "start_pos": 181, "end_pos": 181, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1287790049", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1287790049", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1287790049", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1287790049#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1287790049", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1287790049", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KLQSGTHCLWTDQLLQGSEK", "down_seq": "FQSRHLACLPREPGLCTWQS", "snv": [ { "evidence": [ { "id": "rs1287790049", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1287790049" }, { "id": "rs1287790049", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1287790049#frequency_tab" }, { "id": "rs1287790049", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1287790049" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586609", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G181", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.162.162", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.200.200", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057828202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828202", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057828202", "url": "https://www.ensembl.org/id/rs2057828202", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2057828183", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828183", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057828183", "url": "https://www.ensembl.org/id/rs2057828183", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SGTHCLWTDQLLQGSEKGFQ", "down_seq": "RHLACLPREPGLCTWQSLRS", "snv": [ { "evidence": [ { "id": "rs2057828202", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828202" }, { "id": "rs2057828202", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057828202" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586618", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2057828183", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828183" }, { "id": "rs2057828183", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057828183" } ], "glycoeffect": [], "sequence_org": "S", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586617", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.204.204", "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": 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": "P01033-1.185.185", "start_pos": 185, "end_pos": 185, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs202136502", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202136502", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202136502", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202136502", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs202136502", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202136502", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202136502", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202136502#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs202136502", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202136502", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs141512610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141512610", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141512610", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141512610", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs141512610", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141512610#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs141512610", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141512610", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs141512610", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141512610", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GTHCLWTDQLLQGSEKGFQS", "down_seq": "HLACLPREPGLCTWQSLRSQ", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs202136502", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202136502" }, { "id": "rs202136502", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202136502" }, { "id": "rs202136502", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202136502" }, { "id": "rs202136502", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202136502#frequency_tab" }, { "id": "rs202136502", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202136502" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586620", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R185", "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": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs141512610", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141512610" }, { "id": "rs141512610", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141512610" }, { "id": "rs141512610", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141512610#frequency_tab" }, { "id": "rs141512610", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141512610" }, { "id": "rs141512610", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141512610" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586621", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R185", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586620", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R185", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.205.205", "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": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.186.186", "start_pos": 186, "end_pos": 186, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1046408975", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1046408975", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1046408975", "url": "https://www.ensembl.org/id/rs1046408975", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "THCLWTDQLLQGSEKGFQSR", "down_seq": "LACLPREPGLCTWQSLRSQI", "snv": [ { "evidence": [ { "id": "rs1046408975", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1046408975" }, { "id": "rs1046408975", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1046408975" } ], "glycoeffect": [], "sequence_org": "H", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586623", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H186", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.167.167", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.170.170", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1290911753", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1290911753", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1290911753", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1290911753", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "TDQLLQGSEKGFQSRHLACL", "down_seq": "REPGLCTWQSLRSQIA", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586639", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P191", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1290911753", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1290911753" }, { "id": "rs1290911753", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1290911753" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586639", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P191", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586638", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P191", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.171.171", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.206.206", "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": 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": "P01033-1.192.192", "start_pos": 192, "end_pos": 192, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs149986790", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149986790", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149986790", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149986790", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs149986790", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149986790", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149986790", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149986790#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149986790", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149986790", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs149986790", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149986790", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs192373432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs192373432", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs192373432", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs192373432", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs192373432", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs192373432", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs192373432", "url": "https://www.ncbi.nlm.nih.gov/snp/rs192373432#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs192373432", "url": "http://gnomad.broadinstitute.org/awesome?query=rs192373432", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs192373432", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs192373432", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DQLLQGSEKGFQSRHLACLP", "down_seq": "EPGLCTWQSLRSQIA", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs149986790", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149986790" }, { "id": "rs149986790", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149986790" }, { "id": "rs149986790", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149986790" }, { "id": "rs149986790", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149986790#frequency_tab" }, { "id": "rs149986790", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149986790" }, { "id": "rs149986790", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149986790" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586642", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R192", "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", "ebi" ] }, { "evidence": [ { "id": "rs192373432", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs192373432" }, { "id": "rs192373432", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs192373432" }, { "id": "rs192373432", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs192373432" }, { "id": "rs192373432", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs192373432#frequency_tab" }, { "id": "rs192373432", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs192373432" }, { "id": "rs192373432", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs192373432" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586641", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R192", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "P01033-1.193.193", "start_pos": 193, "end_pos": 193, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1265420217", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265420217", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1265420217", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265420217", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QLLQGSEKGFQSRHLACLPR", "down_seq": "PGLCTWQSLRSQIA", "snv": [ { "evidence": [ { "id": "rs1265420217", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265420217" }, { "id": "rs1265420217", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265420217" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "K", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586644", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E193", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.195.195", "start_pos": 195, "end_pos": 195, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs778252202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778252202", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs778252202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778252202", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs778252202", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778252202", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "LQGSEKGFQSRHLACLPREP", "down_seq": "LCTWQSLRSQIA", "snv": [ { "evidence": [ { "id": "rs778252202", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778252202" }, { "id": "rs778252202", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs778252202" }, { "id": "rs778252202", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs778252202" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586651", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G195", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.176.176", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.178.178", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.179.179", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.19.19", "start_pos": 19, "end_pos": 19, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MAPFEPLASGILLLLWLI", "down_seq": "PSRACTCVPPHPQTAFCNSD", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583470", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A19", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770979056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770979056", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770979056", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770979056", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770979056", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770979056#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs770979056", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770979056", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "KGFQSRHLACLPREPGLCTW", "down_seq": "SLRSQIA", "snv": [ { "evidence": [ { "id": "rs770979056", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770979056" }, { "id": "rs770979056", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770979056" }, { "id": "rs770979056", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs770979056#frequency_tab" }, { "id": "rs770979056", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770979056" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586665", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q200", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.180.180", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.181.181", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.203.203", "start_pos": 203, "end_pos": 203, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs188206458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188206458", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs188206458", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188206458", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs188206458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188206458", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs188206458", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188206458#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs188206458", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188206458", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs188206458", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188206458", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs145224385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145224385", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145224385", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145224385", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145224385", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145224385#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145224385", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145224385", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs145224385", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145224385", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "QSRHLACLPREPGLCTWQSL", "down_seq": "SQIA", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs188206458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188206458" }, { "id": "rs188206458", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188206458" }, { "id": "rs188206458", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs188206458" }, { "id": "rs188206458", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs188206458#frequency_tab" }, { "id": "rs188206458", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs188206458" }, { "id": "rs188206458", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs188206458" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586675", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R203", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs145224385", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145224385" }, { "id": "rs145224385", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145224385" }, { "id": "rs145224385", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145224385#frequency_tab" }, { "id": "rs145224385", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145224385" }, { "id": "rs145224385", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145224385" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47586674", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R203", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": "P01033-1.204.204", "start_pos": 204, "end_pos": 204, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1210534602", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1210534602", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1210534602", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1210534602#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRHLACLPREPGLCTWQSLR", "down_seq": "QIA", "snv": [ { "evidence": [ { "id": "rs1210534602", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1210534602" }, { "id": "rs1210534602", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1210534602#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586677", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S204", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.205.205", "start_pos": 205, "end_pos": 205, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057828582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828582", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057828582", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057828582#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "RHLACLPREPGLCTWQSLRS", "down_seq": "IA", "snv": [ { "evidence": [ { "id": "rs2057828582", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057828582" }, { "id": "rs2057828582", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057828582#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586682", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q205", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.185.185", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.206.206", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.206.206", "start_pos": 206, "end_pos": 206, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775370032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775370032", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775370032", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775370032", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775370032", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775370032", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "HLACLPREPGLCTWQSLRSQ", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs775370032", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775370032" }, { "id": "rs775370032", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775370032" }, { "id": "rs775370032", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775370032" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47586684", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I206", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.186.186", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.191.191", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.192.192", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.193.193", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.195.195", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.200.200", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.203.203", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.204.204", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.205.205", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.20.20", "start_pos": 20, "end_pos": 20, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057808640", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808640", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057808640", "url": "https://www.ensembl.org/id/rs2057808640", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "", "down_seq": "SRACTCVPPHPQTAFCNSDL", "snv": [ { "evidence": [ { "id": "rs2057808640", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808640" }, { "id": "rs2057808640", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057808640" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583474", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P20", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.22.22", "start_pos": 22, "end_pos": 22, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1260941670", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260941670", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1260941670", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260941670#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1260941670", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260941670", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1260941670", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1260941670", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "APFEPLASGILLLLWLIAPS", "down_seq": "ACTCVPPHPQTAFCNSDLVI", "snv": [ { "evidence": [ { "id": "rs1260941670", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1260941670" }, { "id": "rs1260941670", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1260941670#frequency_tab" }, { "id": "rs1260941670", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1260941670" }, { "id": "rs1260941670", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1260941670" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583481", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R22", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.42.42", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs3211164", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3211164", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs3211164", "url": "https://www.ensembl.org/id/rs3211164", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PFEPLASGILLLLWLIAPSR", "down_seq": "CTCVPPHPQTAFCNSDLVIR", "snv": [ { "evidence": [ { "id": "rs3211164", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs3211164" }, { "id": "rs3211164", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs3211164" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583482", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A23", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "PLASGILLLLWLIAPSRACT", "down_seq": "VPPHPQTAFCNSDLVIRAKF", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "C", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583491", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "C26", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LASGILLLLWLIAPSRACTC", "down_seq": "PPHPQTAFCNSDLVIRAKFV", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583495", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "V27", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.28.28", "start_pos": 28, "end_pos": 28, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs372229890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372229890", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs372229890", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372229890", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs372229890", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372229890#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs372229890", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372229890", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ASGILLLLWLIAPSRACTCV", "down_seq": "PHPQTAFCNSDLVIRAKFVG", "snv": [ { "evidence": [ { "id": "rs372229890", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372229890" }, { "id": "rs372229890", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs372229890" }, { "id": "rs372229890", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs372229890#frequency_tab" }, { "id": "rs372229890", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs372229890" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583497", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P28", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583497", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P28", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.48.48", "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": 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": "P01033-1.2.2", "start_pos": 2, "end_pos": 2, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "M", "down_seq": "PFEPLASGILLLLWLIAPSR", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583419", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "A2", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs202175145", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202175145", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs202175145", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202175145", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs202175145", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202175145", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs202175145", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202175145#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs202175145", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202175145", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLLWLIAPSRACTCVPPHPQ", "down_seq": "AFCNSDLVIRAKFVGTPEVN", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs202175145", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202175145" }, { "id": "rs202175145", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs202175145" }, { "id": "rs202175145", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs202175145" }, { "id": "rs202175145", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs202175145#frequency_tab" }, { "id": "rs202175145", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs202175145" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583513", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T33", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.53.53", "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": "P01033-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1310743953", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1310743953", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1310743953", "url": "https://www.ensembl.org/id/rs1310743953", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "LIAPSRACTCVPPHPQTAFC", "down_seq": "SDLVIRAKFVGTPEVNQTTL", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1310743953", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1310743953" }, { "id": "rs1310743953", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1310743953" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583524", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "N37", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs913304425", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs913304425", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs913304425", "url": "https://www.ensembl.org/id/rs913304425", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IAPSRACTCVPPHPQTAFCN", "down_seq": "DLVIRAKFVGTPEVNQTTLY", "snv": [ { "evidence": [ { "id": "rs913304425", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs913304425" }, { "id": "rs913304425", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs913304425" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583528", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S38", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.58.58", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.39.39", "start_pos": 39, "end_pos": 39, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057808892", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808892", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057808892", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057808892#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "APSRACTCVPPHPQTAFCNS", "down_seq": "LVIRAKFVGTPEVNQTTLYQ", "snv": [ { "evidence": [ { "id": "rs2057808892", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808892" }, { "id": "rs2057808892", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057808892#frequency_tab" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583530", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D39", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MA", "down_seq": "FEPLASGILLLLWLIAPSRA", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583422", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P3", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.23.23", "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": "P01033-1.41.41", "start_pos": 41, "end_pos": 41, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "SRACTCVPPHPQTAFCNSDL", "down_seq": "IRAKFVGTPEVNQTTLYQRY", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583536", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V41", "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: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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs758994538", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758994538", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs758994538", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758994538", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs758994538", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758994538", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "RACTCVPPHPQTAFCNSDLV", "down_seq": "RAKFVGTPEVNQTTLYQRYE", "snv": [ { "evidence": [ { "id": "rs758994538", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758994538" }, { "id": "rs758994538", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs758994538" }, { "id": "rs758994538", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs758994538" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584939", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I42", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs780414478", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780414478", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs780414478", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780414478", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs780414478", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780414478", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ACTCVPPHPQTAFCNSDLVI", "down_seq": "AKFVGTPEVNQTTLYQRYEI", "snv": [ { "evidence": [ { "id": "rs780414478", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780414478" }, { "id": "rs780414478", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs780414478" }, { "id": "rs780414478", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs780414478" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584942", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R43", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "CTCVPPHPQTAFCNSDLVIR", "down_seq": "KFVGTPEVNQTTLYQRYEIK", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47584944", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A44", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.64.64", "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": "P01033-1.47.47", "start_pos": 47, "end_pos": 47, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs145937340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145937340", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145937340", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145937340", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs145937340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145937340", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145937340", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145937340#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145937340", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145937340", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VPPHPQTAFCNSDLVIRAKF", "down_seq": "GTPEVNQTTLYQRYEIKMTK", "snv": [ { "evidence": [ { "id": "rs145937340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145937340" }, { "id": "rs145937340", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145937340" }, { "id": "rs145937340", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145937340" }, { "id": "rs145937340", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145937340#frequency_tab" }, { "id": "rs145937340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145937340" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584953", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V47", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs145937340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145937340" }, { "id": "rs145937340", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145937340" }, { "id": "rs145937340", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145937340" }, { "id": "rs145937340", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145937340#frequency_tab" }, { "id": "rs145937340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145937340" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "M", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584953", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V47", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1311258070", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1311258070", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1311258070", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1311258070", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PPHPQTAFCNSDLVIRAKFV", "down_seq": "TPEVNQTTLYQRYEIKMTKM", "snv": [ { "evidence": [ { "id": "rs1311258070", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1311258070" }, { "id": "rs1311258070", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1311258070" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584957", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G48", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.49.49", "start_pos": 49, "end_pos": 49, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs867625040", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867625040", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs867625040", "url": "https://www.ensembl.org/id/rs867625040", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PHPQTAFCNSDLVIRAKFVG", "down_seq": "PEVNQTTLYQRYEIKMTKMY", "snv": [ { "evidence": [ { "id": "rs867625040", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867625040" }, { "id": "rs867625040", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs867625040" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "A", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584959", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T49", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2057808399", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808399", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057808399", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057808399#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "MAP", "down_seq": "EPLASGILLLLWLIAPSRAC", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47583427", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "F4", "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": "rs2057808399", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057808399" }, { "id": "rs2057808399", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057808399#frequency_tab" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583426", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F4", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.23.23", "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": 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": "P01033-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs145349279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145349279", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs145349279", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145349279", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs145349279", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145349279", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs145349279", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145349279#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs145349279", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145349279", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "HPQTAFCNSDLVIRAKFVGT", "down_seq": "EVNQTTLYQRYEIKMTKMYK", "snv": [ { "evidence": [ { "id": "rs145349279", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145349279" }, { "id": "rs145349279", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs145349279" }, { "id": "rs145349279", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs145349279" }, { "id": "rs145349279", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs145349279#frequency_tab" }, { "id": "rs145349279", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs145349279" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584962", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P50", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.30.30", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs141614092", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141614092", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs141614092", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141614092", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs141614092", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141614092", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs141614092", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141614092#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs141614092", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141614092", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PQTAFCNSDLVIRAKFVGTP", "down_seq": "VNQTTLYQRYEIKMTKMYKG", "snv": [ { "evidence": [ { "id": "rs141614092", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141614092" }, { "id": "rs141614092", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs141614092" }, { "id": "rs141614092", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs141614092" }, { "id": "rs141614092", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs141614092#frequency_tab" }, { "id": "rs141614092", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs141614092" } ], "glycoeffect": [], "sequence_org": "E", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584967", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "E51", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.52.52", "start_pos": 52, "end_pos": 52, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1648289847", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1648289847", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1648289847", "url": "https://www.ensembl.org/id/rs1648289847", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "QTAFCNSDLVIRAKFVGTPE", "down_seq": "NQTTLYQRYEIKMTKMYKGF", "snv": [ { "evidence": [ { "id": "rs1648289847", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1648289847" }, { "id": "rs1648289847", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1648289847" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584968", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V52", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.32.32", "categories": [ "mutagenesis_flag", "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057816792", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057816792", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057816792", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057816792#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NSDLVIRAKFVGTPEVNQTT", "down_seq": "YQRYEIKMTKMYKGFQALGD", "snv": [ { "evidence": [ { "id": "rs2057816792", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057816792" }, { "id": "rs2057816792", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057816792#frequency_tab" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584984", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L57", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.37.37", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.77.77", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1301268711", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1301268711", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1301268711", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1301268711#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1301268711", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1301268711", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SDLVIRAKFVGTPEVNQTTL", "down_seq": "QRYEIKMTKMYKGFQALGDA", "snv": [ { "evidence": [ { "id": "rs1301268711", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1301268711" }, { "id": "rs1301268711", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1301268711#frequency_tab" }, { "id": "rs1301268711", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1301268711" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584986", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y58", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1469640098", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469640098", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1469640098", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469640098#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "DLVIRAKFVGTPEVNQTTLY", "down_seq": "RYEIKMTKMYKGFQALGDAA", "snv": [ { "evidence": [ { "id": "rs1469640098", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469640098" }, { "id": "rs1469640098", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469640098#frequency_tab" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584990", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q59", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.39.39", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs769724738", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769724738", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs769724738", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769724738", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs769724738", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769724738#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs769724738", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769724738", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs769724738", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769724738", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs762640736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762640736", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762640736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762640736", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762640736", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762640736", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LVIRAKFVGTPEVNQTTLYQ", "down_seq": "YEIKMTKMYKGFQALGDAAD", "snv": [ { "evidence": [ { "id": "rs769724738", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769724738" }, { "id": "rs769724738", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769724738" }, { "id": "rs769724738", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769724738#frequency_tab" }, { "id": "rs769724738", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769724738" }, { "id": "rs769724738", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769724738" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584992", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R60", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs762640736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762640736" }, { "id": "rs762640736", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762640736" }, { "id": "rs762640736", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762640736" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584993", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R60", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs769724738", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769724738" }, { "id": "rs769724738", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs769724738" }, { "id": "rs769724738", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs769724738#frequency_tab" }, { "id": "rs769724738", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs769724738" }, { "id": "rs769724738", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs769724738" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47584992", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R60", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.41.41", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.43.43", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P01033-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs971300087", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs971300087", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs971300087", "url": "https://www.ensembl.org/id/rs971300087", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "AKFVGTPEVNQTTLYQRYEI", "down_seq": "MTKMYKGFQALGDAADIRFV", "snv": [ { "evidence": [ { "id": "rs971300087", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs971300087" }, { "id": "rs971300087", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs971300087" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585005", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K64", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.65.65", "start_pos": 65, "end_pos": 65, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs61756234", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61756234", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61756234", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61756234", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61756234", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61756234#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61756234", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61756234", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "KFVGTPEVNQTTLYQRYEIK", "down_seq": "TKMYKGFQALGDAADIRFVY", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs61756234", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61756234" }, { "id": "rs61756234", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61756234" }, { "id": "rs61756234", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61756234#frequency_tab" }, { "id": "rs61756234", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61756234" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585009", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "M65", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.47.47", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770619788", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770619788", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770619788", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770619788", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770619788", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770619788", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1569325736", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1569325736", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1569325736", "url": "https://www.ensembl.org/id/rs1569325736", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs749176055", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749176055", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749176055", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749176055", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749176055", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749176055#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs749176055", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749176055", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "GTPEVNQTTLYQRYEIKMTK", "down_seq": "YKGFQALGDAADIRFVYTPA", "snv": [ { "evidence": [ { "id": "rs770619788", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770619788" }, { "id": "rs770619788", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770619788" }, { "id": "rs770619788", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770619788" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585207", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M68", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1569325736", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1569325736" }, { "id": "rs1569325736", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1569325736" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585206", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M68", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs749176055", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749176055" }, { "id": "rs749176055", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749176055" }, { "id": "rs749176055", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs749176055#frequency_tab" }, { "id": "rs749176055", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749176055" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585205", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M68", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P01033-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs774396901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774396901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774396901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774396901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774396901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774396901", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TPEVNQTTLYQRYEIKMTKM", "down_seq": "KGFQALGDAADIRFVYTPAM", "snv": [ { "evidence": [ { "id": "rs774396901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774396901" }, { "id": "rs774396901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774396901" }, { "id": "rs774396901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774396901" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585208", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y69", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs774396901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774396901" }, { "id": "rs774396901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774396901" }, { "id": "rs774396901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774396901" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585208", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y69", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.49.49", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1475267344", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475267344", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1475267344", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475267344#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "MAPFE", "down_seq": "LASGILLLLWLIAPSRACTC", "snv": [ { "evidence": [ { "id": "rs1475267344", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1475267344" }, { "id": "rs1475267344", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1475267344#frequency_tab" } ], "glycoeffect": [], "sequence_org": "P", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583432", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P6", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057818128", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057818128", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057818128", "url": "https://www.ensembl.org/id/rs2057818128", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PEVNQTTLYQRYEIKMTKMY", "down_seq": "GFQALGDAADIRFVYTPAME", "snv": [ { "evidence": [ { "id": "rs2057818128", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057818128" }, { "id": "rs2057818128", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057818128" } ], "glycoeffect": [], "sequence_org": "K", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585212", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K70", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1041922373", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1041922373", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1041922373", "url": "https://www.ensembl.org/id/rs1041922373", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "VNQTTLYQRYEIKMTKMYKG", "down_seq": "QALGDAADIRFVYTPAMESV", "snv": [ { "evidence": [ { "id": "rs1041922373", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1041922373" }, { "id": "rs1041922373", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1041922373" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "L", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585217", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F72", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585218", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "F72", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.52.52", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P01033-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1443688748", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443688748", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443688748", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1443688748#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1443688748", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443688748", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1248254190", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248254190", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1248254190", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1248254190#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1248254190", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1248254190", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "NQTTLYQRYEIKMTKMYKGF", "down_seq": "ALGDAADIRFVYTPAMESVC", "snv": [ { "evidence": [ { "id": "rs1443688748", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443688748" }, { "id": "rs1443688748", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1443688748#frequency_tab" }, { "id": "rs1443688748", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443688748" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585220", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q73", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1248254190", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248254190" }, { "id": "rs1248254190", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1248254190#frequency_tab" }, { "id": "rs1248254190", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1248254190" } ], "glycoeffect": [], "sequence_org": "Q", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585221", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Q73", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.53.53", "categories": [ "glycosylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QTTLYQRYEIKMTKMYKGFQ", "down_seq": "LGDAADIRFVYTPAMESVCG", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585224", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A74", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.75.75", "start_pos": 75, "end_pos": 75, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1190276304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1190276304", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1190276304", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1190276304#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1190276304", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1190276304", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "TTLYQRYEIKMTKMYKGFQA", "down_seq": "GDAADIRFVYTPAMESVCGY", "snv": [ { "evidence": [ { "id": "rs1190276304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1190276304" }, { "id": "rs1190276304", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1190276304#frequency_tab" }, { "id": "rs1190276304", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1190276304" } ], "glycoeffect": [], "sequence_org": "L", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585227", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "L75", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745761692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745761692", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745761692", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745761692", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745761692", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745761692#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs745761692", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745761692", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs182947561", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs182947561", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs182947561", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs182947561", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs182947561", "url": "https://www.ncbi.nlm.nih.gov/snp/rs182947561#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs182947561", "url": "http://gnomad.broadinstitute.org/awesome?query=rs182947561", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TLYQRYEIKMTKMYKGFQAL", "down_seq": "DAADIRFVYTPAMESVCGYF", "snv": [ { "evidence": [ { "id": "rs745761692", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745761692" }, { "id": "rs745761692", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745761692" }, { "id": "rs745761692", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs745761692#frequency_tab" }, { "id": "rs745761692", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745761692" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "E", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585230", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G76", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs182947561", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs182947561" }, { "id": "rs182947561", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs182947561" }, { "id": "rs182947561", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs182947561#frequency_tab" }, { "id": "rs182947561", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs182947561" } ], "glycoeffect": [], "sequence_org": "G", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585229", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G76", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585230", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G76", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.96.96", "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": 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": "P01033-1.77.77", "start_pos": 77, "end_pos": 77, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs761153618", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761153618", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs761153618", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761153618", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs761153618", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761153618", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs761153618", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761153618", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LYQRYEIKMTKMYKGFQALG", "down_seq": "AADIRFVYTPAMESVCGYFH", "snv": [ { "evidence": [ { "id": "rs761153618", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761153618" }, { "id": "rs761153618", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs761153618" }, { "id": "rs761153618", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs761153618" }, { "id": "rs761153618", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs761153618" } ], "glycoeffect": [], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585232", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D77", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.57.57", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1336825386", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1336825386", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1336825386", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1336825386#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1336825386", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1336825386", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "YQRYEIKMTKMYKGFQALGD", "down_seq": "ADIRFVYTPAMESVCGYFHR", "snv": [ { "evidence": [ { "id": "rs1336825386", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1336825386" }, { "id": "rs1336825386", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1336825386#frequency_tab" }, { "id": "rs1336825386", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1336825386" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585236", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A78", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.59.59", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2057818338", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057818338", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057818338", "url": "https://www.ensembl.org/id/rs2057818338", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "YEIKMTKMYKGFQALGDAAD", "down_seq": "RFVYTPAMESVCGYFHRSHN", "snv": [ { "evidence": [ { "id": "rs2057818338", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057818338" }, { "id": "rs2057818338", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2057818338" } ], "glycoeffect": [], "sequence_org": "I", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585245", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I81", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.101.101", "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": "P01033-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760118306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760118306", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760118306", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760118306", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760118306", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760118306#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760118306", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760118306", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs776140969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776140969", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776140969", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776140969", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776140969", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776140969", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EIKMTKMYKGFQALGDAADI", "down_seq": "FVYTPAMESVCGYFHRSHNR", "snv": [ { "evidence": [ { "id": "rs760118306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760118306" }, { "id": "rs760118306", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760118306" }, { "id": "rs760118306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760118306#frequency_tab" }, { "id": "rs760118306", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760118306" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "G", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585247", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R82", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776140969", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776140969" }, { "id": "rs776140969", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776140969" }, { "id": "rs776140969", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776140969" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "Q", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585248", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R82", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs760118306", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760118306" }, { "id": "rs760118306", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760118306" }, { "id": "rs760118306", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760118306#frequency_tab" }, { "id": "rs760118306", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760118306" } ], "glycoeffect": [], "sequence_org": "R", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585247", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R82", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1265435772", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265435772", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1265435772", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265435772", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1265435772", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1265435772", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "KMTKMYKGFQALGDAADIRF", "down_seq": "YTPAMESVCGYFHRSHNRSE", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1265435772", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1265435772" }, { "id": "rs1265435772", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1265435772" }, { "id": "rs1265435772", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1265435772" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585253", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "V84", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.65.65", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.104.104", "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": "P01033-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1187897994", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187897994", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1187897994", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1187897994", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "TKMYKGFQALGDAADIRFVY", "down_seq": "PAMESVCGYFHRSHNRSEEF", "snv": [ { "evidence": [ { "id": "rs1187897994", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1187897994" }, { "id": "rs1187897994", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1187897994" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "P", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585259", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T86", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1476457782", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1476457782", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1476457782", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1476457782", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1476457782", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1476457782", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MYKGFQALGDAADIRFVYTP", "down_seq": "MESVCGYFHRSHNRSEEFLI", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1476457782", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1476457782" }, { "id": "rs1476457782", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1476457782" }, { "id": "rs1476457782", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1476457782" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585265", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A88", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.89.89", "start_pos": 89, "end_pos": 89, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1226680303", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226680303", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1226680303", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1226680303#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1226680303", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1226680303", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2057818580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057818580", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2057818580", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057818580#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs2057818580", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2057818580", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2057818580", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2057818580", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs1300025986", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1300025986", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1300025986", "url": "https://www.ensembl.org/id/rs1300025986", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "YKGFQALGDAADIRFVYTPA", "down_seq": "ESVCGYFHRSHNRSEEFLIA", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1226680303", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1226680303" }, { "id": "rs1226680303", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1226680303#frequency_tab" }, { "id": "rs1226680303", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1226680303" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585270", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "M89", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] }, { "evidence": [ { "id": "rs2057818580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2057818580" }, { "id": "rs2057818580", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2057818580#frequency_tab" }, { "id": "rs2057818580", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs2057818580" }, { "id": "rs2057818580", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2057818580" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585269", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M89", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1300025986", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1300025986" }, { "id": "rs1300025986", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1300025986" } ], "glycoeffect": [], "sequence_org": "M", "sequence_mut": "V", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585268", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M89", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P01033-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs369537887", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369537887", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs369537887", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369537887", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs369537887", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369537887#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs369537887", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369537887", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "MAPFEPL", "down_seq": "SGILLLLWLIAPSRACTCVP", "snv": [ { "evidence": [ { "id": "rs369537887", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369537887" }, { "id": "rs369537887", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs369537887" }, { "id": "rs369537887", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs369537887#frequency_tab" }, { "id": "rs369537887", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs369537887" } ], "glycoeffect": [], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583437", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A8", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.9.9", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.92.92", "start_pos": 92, "end_pos": 92, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1324579667", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324579667", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1324579667", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1324579667#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1324579667", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324579667", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "FQALGDAADIRFVYTPAMES", "down_seq": "CGYFHRSHNRSEEFLIAGKL", "snv": [ { "evidence": [ { "id": "rs1324579667", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1324579667" }, { "id": "rs1324579667", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1324579667#frequency_tab" }, { "id": "rs1324579667", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1324579667" } ], "glycoeffect": [], "sequence_org": "V", "sequence_mut": "D", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585278", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "V92", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.110.110", "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": "P01033-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "QALGDAADIRFVYTPAMESV", "down_seq": "GYFHRSHNRSEEFLIAGKLQ", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585281", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "C93", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.73.73", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1319834840", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1319834840", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1319834840", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1319834840#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1319834840", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1319834840", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1319834840", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1319834840", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ALGDAADIRFVYTPAMESVC", "down_seq": "YFHRSHNRSEEFLIAGKLQD", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1319834840", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1319834840" }, { "id": "rs1319834840", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1319834840#frequency_tab" }, { "id": "rs1319834840", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1319834840" }, { "id": "rs1319834840", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1319834840" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585283", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G94", "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": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.75.75", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.96.96", "start_pos": 96, "end_pos": 96, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1360628820", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360628820", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1360628820", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360628820", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "GDAADIRFVYTPAMESVCGY", "down_seq": "HRSHNRSEEFLIAGKLQDGL", "snv": [ { "evidence": [ { "id": "rs1360628820", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360628820" }, { "id": "rs1360628820", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360628820" } ], "glycoeffect": [], "sequence_org": "F", "sequence_mut": "I", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585289", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F96", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.97.97", "start_pos": 97, "end_pos": 97, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P01033", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1413685629", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413685629", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1413685629", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413685629#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1413685629", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413685629", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "DAADIRFVYTPAMESVCGYF", "down_seq": "RSHNRSEEFLIAGKLQDGLL", "snv": [ { "evidence": [ { "id": "P01033", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P01033" }, { "id": "rs1413685629", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1413685629" }, { "id": "rs1413685629", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1413685629#frequency_tab" }, { "id": "rs1413685629", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1413685629" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: protein-of-interest(glycogene, tissue inhibitor of matrix metalloproteinase).", "chr_id": "23", "chr_pos": "47585292", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H97", "disease": [ { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P01033-1.77.77", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P01033-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.99.99", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P01033-1.99.99", "start_pos": 99, "end_pos": 99, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752832099", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752832099", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752832099", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752832099", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs752832099", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752832099", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ADIRFVYTPAMESVCGYFHR", "down_seq": "HNRSEEFLIAGKLQDGLLHI", "snv": [ { "evidence": [ { "id": "rs752832099", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752832099" }, { "id": "rs752832099", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752832099" }, { "id": "rs752832099", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752832099" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "F", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47585299", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S99", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P01033-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P01033-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P01033-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P01033-1.86.86", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P01033-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P01033-1.89.89", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.92.92", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.96.96", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P01033-1.97.97", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.100.100", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P01033-1.101.101", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P01033-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P01033-1.104.104", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P01033-1.105.105", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P01033-1.107.107", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P01033-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.113.113", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P01033-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.115.115", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.118.118", "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": "P01033-1.9.9", "start_pos": 9, "end_pos": 9, "uniprot_canonical_ac": "P01033-1", "length": 207, "uniprot_id": "TIMP1_HUMAN", "protein_name": "Metalloproteinase inhibitor 1", "refseq_ac": "NP_003245", "refseq_name": "metalloproteinase inhibitor 1 precursor", "gene_name": "TIMP1", "gene_names_uniprotkb": "TIMP1; CLGI; TIMP", "gene_names_refseq": "CLGI; EPA; EPO; HCI; TIMP-1; TIMP1; TIMP", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P01033", "url": "https://www.uniprot.org/uniprotkb/P01033" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1482757210", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482757210", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1482757210", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1482757210#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MAPFEPLA", "down_seq": "GILLLLWLIAPSRACTCVPP", "snv": [ { "evidence": [ { "id": "rs1482757210", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1482757210" }, { "id": "rs1482757210", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1482757210#frequency_tab" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "Y", "comment": "Germline mutation passed 1 filters: glycogene of type=glycogene, tissue inhibitor of matrix metalloproteinase.", "chr_id": "X", "chr_pos": "47583441", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S9", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "53", "end_pos": "53" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "121", "end_pos": "121" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "30", "end_pos": "30" }, { "start_pos": "32", "end_pos": "32" } ] }, { "type": "snv", "site_list": [ { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "171", "end_pos": "171" }, { "start_pos": "100", "end_pos": "100" }, { "start_pos": "104", "end_pos": "104" }, { "start_pos": "105", "end_pos": "105" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "107", "end_pos": "107" }, { "start_pos": "108", "end_pos": "108" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "118", "end_pos": "118" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "123", "end_pos": "123" }, { "start_pos": "124", "end_pos": "124" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "127", "end_pos": "127" }, { "start_pos": "128", "end_pos": "128" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "132", "end_pos": "132" }, { "start_pos": "134", "end_pos": "134" }, { "start_pos": "135", "end_pos": "135" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "138", "end_pos": "138" }, { "start_pos": "140", "end_pos": "140" }, { "start_pos": "141", "end_pos": "141" }, { "start_pos": "142", "end_pos": "142" }, { "start_pos": "144", "end_pos": "144" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "148", "end_pos": "148" }, { "start_pos": "151", "end_pos": "151" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "154", "end_pos": "154" }, { "start_pos": "156", "end_pos": "156" }, { "start_pos": "157", "end_pos": "157" }, { "start_pos": "159", "end_pos": "159" }, { "start_pos": "160", "end_pos": "160" }, { "start_pos": "162", "end_pos": "162" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "16", "end_pos": "16" }, { "start_pos": "170", "end_pos": "170" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "178", "end_pos": "178" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "185", "end_pos": "185" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "193", "end_pos": "193" }, { "start_pos": "195", "end_pos": "195" }, { "start_pos": "19", "end_pos": "19" }, { "start_pos": "200", "end_pos": "200" }, { "start_pos": "203", "end_pos": "203" }, { "start_pos": "204", "end_pos": "204" }, { "start_pos": "205", "end_pos": "205" }, { "start_pos": "206", "end_pos": "206" }, { "start_pos": "20", "end_pos": "20" }, { "start_pos": "22", "end_pos": "22" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "26", "end_pos": "26" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "28", "end_pos": "28" }, { "start_pos": "2", "end_pos": "2" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "37", "end_pos": "37" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "39", "end_pos": "39" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "41", "end_pos": "41" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "47", "end_pos": "47" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "49", "end_pos": "49" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "52", "end_pos": "52" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "65", "end_pos": "65" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "6", "end_pos": "6" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "73", "end_pos": "73" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "75", "end_pos": "75" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "77", "end_pos": "77" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "86", "end_pos": "86" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "89", "end_pos": "89" }, { "start_pos": "8", "end_pos": "8" }, { "start_pos": "92", "end_pos": "92" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "96", "end_pos": "96" }, { "start_pos": "97", "end_pos": "97" }, { "start_pos": "99", "end_pos": "99" }, { "start_pos": "9", "end_pos": "9" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "178", "end_pos": "178" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P01033-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P01033-1.2.2", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P01033-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P01033-1.4.4", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P01033-1.6.6", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P01033-1.8.8", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P01033-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P01033-1.16.16", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P01033-1.19.19", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P01033-1.20.20", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P01033-1.22.22", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P01033-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P01033-1.25.25", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P01033-1.26.26", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P01033-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P01033-1.28.28", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6ZUT1-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZUT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZUT1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "REKKAHTSVANNEIQERTNK", "down_seq": "TNWKVATDERSAESSEDD", "snv": [ { "evidence": [ { "id": "Q6ZUT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZUT1" } ], "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": "11", "chr_pos": "112082914", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R274", "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: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": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "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": "Q6ZUT1-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZUT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZUT1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MS", "down_seq": "IPLGKVLLRNVIRHTDAHNK", "snv": [ { "evidence": [ { "id": "Q6ZUT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZUT1" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "112075582", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R3", "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": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "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": "Q6ZUT1-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZUT1", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZUT1", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KQMEDAYRGTKRKMLPSSSS", "down_seq": "MRSDGFDEESQRYYWRPKNE", "snv": [ { "evidence": [ { "id": "Q6ZUT1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZUT1" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "11", "chr_pos": "112080411", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R58", "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": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q6ZUT1-1.68.68", "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": "Q6ZUT1-1.123.123", "start_pos": 123, "end_pos": 123, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "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": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] } ], "crossref": [ { "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NMPDRWGHSGYKELYPEEFE", "down_seq": "DSDQQDITNGKKTSPQVKSS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" }, { "database": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ], "site_lbl": "Thr123" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q6ZUT1-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6ZUT1-1.136.136", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6ZUT1-1.137.137", "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": "Q6ZUT1-1.125.125", "start_pos": 125, "end_pos": 125, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "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": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] } ], "crossref": [ { "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PDRWGHSGYKELYPEEFETD", "down_seq": "DQQDITNGKKTSPQVKSSTH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" }, { "database": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" }, { "database": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ], "site_lbl": "Ser125" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6ZUT1-1.123.123", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6ZUT1-1.136.136", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6ZUT1-1.137.137", "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": "Q6ZUT1-1.136.136", "start_pos": 136, "end_pos": 136, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "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": "Q6ZUT1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1", "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": "LYPEEFETDSDQQDITNGKK", "down_seq": "SPQVKSSTHESRKHKKSKKS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr136" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6ZUT1-1.123.123", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6ZUT1-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6ZUT1-1.137.137", "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": "Q6ZUT1-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "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": "Q6ZUT1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1", "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": "YPEEFETDSDQQDITNGKKT", "down_seq": "PQVKSSTHESRKHKKSKKSH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser137" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6ZUT1-1.123.123", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6ZUT1-1.125.125", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6ZUT1-1.136.136", "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": "Q6ZUT1-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "Q6ZUT1-1", "length": 292, "uniprot_id": "NKAP1_HUMAN", "protein_name": "Uncharacterized protein NKAPD1", "refseq_ac": "NP_001076439", "refseq_name": "uncharacterized protein NKAPD1 isoform b", "gene_name": "NKAPD1", "gene_names_uniprotkb": "NKAPD1; C11orf57", "gene_names_refseq": "Ahed; C11orf57; NKAPD1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZUT1", "url": "https://www.uniprot.org/uniprotkb/Q6ZUT1" } ], "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": "iPTMnet", "id": "Q6ZUT1-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1-1" } ], "reference": [ { "type": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ] } ], "crossref": [ { "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1", "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": "KRKMLPSSSSRMRSDGFDEE", "down_seq": "QRYYWRPKNEISGTLEDDFL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q6ZUT1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6ZUT1" }, { "database": "PubMed", "id": "17525332", "url": "https://glygen.org/publication/PubMed/17525332" } ], "site_lbl": "Ser68" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "274", "end_pos": "274" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "58", "end_pos": "58" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "123", "end_pos": "123" }, { "start_pos": "125", "end_pos": "125" }, { "start_pos": "136", "end_pos": "136" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "68", "end_pos": "68" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6ZUT1-1.58.58", "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": "A2RUB6-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "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": "A2RUB6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RUB6" } ], "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": "A2RUB6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RUB6", "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": "A2RUB6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=A2RUB6" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "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": "A2RUB6-1.208.948", "start_pos": 208, "end_pos": 948, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The centriolar satellite protein CCDC66 interacts with CEP290 and functions in cilium formation and trafficking.", "journal": "Journal of cell science", "date": "2017", "authors": "Conkar D, Culfa E, Odabasi E, Rauniyar N, Yates JR 3rd, Firat-Karalar EN", "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" }, { "database": "RefSeq", "id": "NP_001012524", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001012524" } ], "reference": [ { "type": "PubMed", "id": "28235840", "url": "https://glygen.org/publication/PubMed/28235840" } ] } ], "crossref": [ { "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "28235840", "url": "https://glygen.org/publication/PubMed/28235840", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "EMVSSVPAENKSVLNEHQETSKQCEQKIAIENEWKPADIFSTLGERECDRSSLEAKKAQWRKELDEQVALKKKEKEVSEKWNDPWKKSESDKIIWEKHQILDQSRETVLLEHPFSAVKQELQRKWIEELNKQIEDDRQRKIEEKIIYSKGEEHDRWAMHFDSLKSYPGSQSQLFSQSTHKQPEYFCVSPDTQELADVSSVCTPTTGSQVEPSEEEHIAKPIKDVVMANSKKTNFLRSMTALLDPAQIEERDRRRQKQLEHQKAITAQVEEKRRKKQLEEEQRKKEEQEEELRLAQEREEMQKQYEEDILKQKQKEEIMTLKTNELFQTMQRAQELAQRLKQEQRIRELAQKGHDTSRLIKNLGVDTIQMEYNASNISNSRHDSDEISGKMNTYMNSTTSKKDTGVQTDDLNIGIFTNAESHCGSLMERDITNCSSPEISAELIGQFSTKKNKQELTQDKGASLEKENNRCNDQCNQFTRIEKQTKHMKKYPKRPDWNINKPPKRYIPASEKYPKQLQKQREEKKVRRQMELLHLVEKNNPGHLSQNRGISPEIFHSSHQETESKLRWHLVKKEEEPLNIHSFSKERSPSSPVPVVKNRTQQTQNTLHLPLKNSSYERENLISGSNQTELSSGISESSHFIPYVRTNEIYYLDPDAPLSGPSTQDPQYQNSQDCGQKRQLFDSDCVRDPLLNPNMVKNRDRQQAILKGLSELRQGLLQKQKELESSLLPLAENQEESFGSSF", "start_aa": "E", "up_seq": "LNSISNQPKDENIMGLFKKT", "down_seq": "", "mutagenesis": [ { "sequence_org": "EMVSSVPAENKSVLNEHQETSKQCEQKIAIENEWKPADIFSTLGERECDRSSLEAKKAQWRKELDEQVALKKKEKEVSEKWNDPWKKSESDKIIWEKHQILDQSRETVLLEHPFSAVKQELQRKWIEELNKQIEDDRQRKIEEKIIYSKGEEHDRWAMHFDSLKSYPGSQSQLFSQSTHKQPEYFCVSPDTQELADVSSVCTPTTGSQVEPSEEEHIAKPIKDVVMANSKKTNFLRSMTALLDPAQIEERDRRRQKQLEHQKAITAQVEEKRRKKQLEEEQRKKEEQEEELRLAQEREEMQKQYEEDILKQKQKEEIMTLKTNELFQTMQRAQELAQRLKQEQRIRELAQKGHDTSRLIKNLGVDTIQMEYNASNISNSRHDSDEISGKMNTYMNSTTSKKDTGVQTDDLNIGIFTNAESHCGSLMERDITNCSSPEISAELIGQFSTKKNKQELTQDKGASLEKENNRCNDQCNQFTRIEKQTKHMKKYPKRPDWNINKPPKRYIPASEKYPKQLQKQREEKKVRRQMELLHLVEKNNPGHLSQNRGISPEIFHSSHQETESKLRWHLVKKEEEPLNIHSFSKERSPSSPVPVVKNRTQQTQNTLHLPLKNSSYERENLISGSNQTELSSGISESSHFIPYVRTNEIYYLDPDAPLSGPSTQDPQYQNSQDCGQKRQLFDSDCVRDPLLNPNMVKNRDRQQAILKGLSELRQGLLQKQKELESSLLPLAENQEESFGSSF", "sequence_mut": "", "comment": "Loss of association with microtubules and localization to centrosomes.", "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" }, { "database": "PubMed", "id": "28235840", "url": "https://glygen.org/publication/PubMed/28235840" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "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": "A2RUB6-1.443.443", "start_pos": 443, "end_pos": 443, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RUB6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RUB6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "HIAKPIKDVVMANSKKTNFL", "down_seq": "SMTALLDPAQIEERDRRRQK", "snv": [ { "evidence": [ { "id": "A2RUB6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RUB6" } ], "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": "3", "chr_pos": "56593951", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R443", "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": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "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": "A2RUB6-1.605.605", "start_pos": 605, "end_pos": 605, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RUB6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RUB6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSRHDSDEISGKMNTYMNST", "down_seq": "SKKDTGVQTDDLNIGIFTNA", "snv": [ { "evidence": [ { "id": "A2RUB6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/A2RUB6" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "3", "chr_pos": "56616023", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T605", "disease": [ { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "A2RUB6-1.606.606", "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": "A2RUB6-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "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": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" }, { "database": "iPTMnet", "id": "A2RUB6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RUB6" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RUB6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RUB6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LCKQCIDKDCLHIQKEISPA", "down_seq": "PNMQKTRNTVNTSLVGKQKP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "A2RUB6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RUB6" } ], "site_lbl": "Thr115" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "A2RUB6-1.121.121", "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": "A2RUB6-1.121.121", "start_pos": 121, "end_pos": 121, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "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": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" }, { "database": "iPTMnet", "id": "A2RUB6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RUB6" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "A2RUB6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RUB6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "DKDCLHIQKEISPATPNMQK", "down_seq": "RNTVNTSLVGKQKPHKKHIT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "A2RUB6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/A2RUB6" } ], "site_lbl": "Thr121" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "A2RUB6-1.115.115", "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": "A2RUB6-1.369.369", "start_pos": 369, "end_pos": 369, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EEKIIYSKGEEHDRWAMHFD", "down_seq": "LKSYPGSQSQLFSQSTHKQP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "site_lbl": "Ser369" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "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": "A2RUB6-1.606.606", "start_pos": 606, "end_pos": 606, "uniprot_canonical_ac": "A2RUB6-1", "length": 948, "uniprot_id": "CCD66_HUMAN", "protein_name": "Coiled-coil domain-containing protein 66", "refseq_ac": "NP_001012524", "refseq_name": "coiled-coil domain-containing protein 66 isoform 2", "gene_name": "CCDC66", "gene_names_uniprotkb": "CCDC66", "gene_names_refseq": "CCDC66", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SRHDSDEISGKMNTYMNSTT", "down_seq": "KKDTGVQTDDLNIGIFTNAE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "A2RUB6", "url": "https://www.uniprot.org/uniprotkb/A2RUB6" } ], "site_lbl": "Ser606" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "208", "end_pos": "948" } ] }, { "type": "snv", "site_list": [ { "start_pos": "443", "end_pos": "443" }, { "start_pos": "605", "end_pos": "605" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "115", "end_pos": "115" }, { "start_pos": "121", "end_pos": "121" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "606", "end_pos": "606" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "A2RUB6-1.605.605", "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": "Q6ZP65-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q6ZP65-1", "length": 573, "uniprot_id": "BICL1_HUMAN", "protein_name": "BICD family-like cargo adapter 1", "refseq_ac": "NP_997194", "refseq_name": "BICD family-like cargo adapter 1 isoform 1", "gene_name": "BICDL1", "gene_names_uniprotkb": "BICDL1; BICDR1; CCDC64", "gene_names_refseq": "BICDL1; BICDR-1; BICDR1; CCDC64A; CCDC64; H_267D11.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZP65", "url": "https://www.uniprot.org/uniprotkb/Q6ZP65" } ], "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": "Q6ZP65", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZP65" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6ZP65", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZP65", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q6ZP65", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6ZP65" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "261", "end_pos": "261" }, { "start_pos": "376", "end_pos": "376" } ] } ], "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": "Q6ZP65-1.261.261", "start_pos": 261, "end_pos": 261, "uniprot_canonical_ac": "Q6ZP65-1", "length": 573, "uniprot_id": "BICL1_HUMAN", "protein_name": "BICD family-like cargo adapter 1", "refseq_ac": "NP_997194", "refseq_name": "BICD family-like cargo adapter 1 isoform 1", "gene_name": "BICDL1", "gene_names_uniprotkb": "BICDL1; BICDR1; CCDC64", "gene_names_refseq": "BICDL1; BICDR-1; BICDR1; CCDC64A; CCDC64; H_267D11.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZP65", "url": "https://www.uniprot.org/uniprotkb/Q6ZP65" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZP65", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZP65", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TNQHIIRLESLQAEIKMLSD", "down_seq": "KRELEHRLSATLEENDLLQG", "snv": [ { "evidence": [ { "id": "Q6ZP65", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZP65" } ], "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": "12", "chr_pos": "120064751", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R261", "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": "snv", "site_list": [ { "start_pos": "261", "end_pos": "261" }, { "start_pos": "376", "end_pos": "376" } ] } ], "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": "Q6ZP65-1.376.376", "start_pos": 376, "end_pos": 376, "uniprot_canonical_ac": "Q6ZP65-1", "length": 573, "uniprot_id": "BICL1_HUMAN", "protein_name": "BICD family-like cargo adapter 1", "refseq_ac": "NP_997194", "refseq_name": "BICD family-like cargo adapter 1 isoform 1", "gene_name": "BICDL1", "gene_names_uniprotkb": "BICDL1; BICDR1; CCDC64", "gene_names_refseq": "BICDL1; BICDR-1; BICDR1; CCDC64A; CCDC64; H_267D11.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6ZP65", "url": "https://www.uniprot.org/uniprotkb/Q6ZP65" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6ZP65", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZP65", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ELEQEREQLRLQLWEAYCQV", "down_seq": "YLCSHLRGNDSADSAVSTDS", "snv": [ { "evidence": [ { "id": "Q6ZP65", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6ZP65" } ], "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": "12", "chr_pos": "120072547", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R376", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "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": "261", "end_pos": "261" }, { "start_pos": "376", "end_pos": "376" } ] } ], "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": "Q8WYA6-1.409.409", "start_pos": 409, "end_pos": 409, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" }, { "database": "O-GlcNAc Atlas", "id": "Q8WYA6", "url": "https://oglcnac.org/atlas/detail/Q8WYA6" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6", "database": "O-GlcNAc Database", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WYA6", "url": "https://oglcnac.org/atlas/detail/Q8WYA6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1446320372", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1446320372", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1446320372", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1446320372#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1446320372", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1446320372", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1446320372", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1446320372", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPRKIKKVGTTEKEHEEHVC", "down_seq": "ILASLLRNLRGQQRTRLLNK", "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": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q8WYA6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" }, { "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q8WYA6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8WYA6" } ] } ], "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" }, { "id": "rs1446320372", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1446320372" }, { "id": "rs1446320372", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1446320372#frequency_tab" }, { "id": "rs1446320372", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1446320372" }, { "id": "rs1446320372", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1446320372" } ], "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: o-glyco-site-loss (S->L).", "chr_id": "20", "chr_pos": "37840114", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S409", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q8WYA6-1.389.389", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WYA6-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" }, { "database": "O-GlcNAc Atlas", "id": "Q8WYA6", "url": "https://oglcnac.org/atlas/detail/Q8WYA6" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WYA6", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6", "database": "O-GlcNAc Database", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WYA6", "url": "https://oglcnac.org/atlas/detail/Q8WYA6", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2072291852", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2072291852", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2072291852", "url": "https://www.ensembl.org/id/rs2072291852", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LASLLRNLRGQQRTRLLNKF", "down_seq": "ENDSEKVDRLMELHFKYLGA", "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": "Thr431", "evidence": [ { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" }, { "id": "Q8WYA6", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8WYA6" }, { "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": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q8WYA6", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8WYA6" } ] } ], "snv": [ { "evidence": [ { "id": "rs2072291852", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2072291852" }, { "id": "rs2072291852", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2072291852" } ], "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": "20", "chr_pos": "37840179", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T431", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8WYA6-1.430.430", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8WYA6-1.16.33", "start_pos": 16, "end_pos": 33, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Interaction between antibody-diversification enzyme AID and spliceosome-associated factor CTNNBL1.", "journal": "Molecular cell", "date": "2008", "authors": "Conticello SG, Ganesh K, Xue K, Lu M, Rada C, Neuberger MS", "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "RefSeq", "id": "NP_001268424", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001268424" } ], "reference": [ { "type": "PubMed", "id": "18722174", "url": "https://glygen.org/publication/PubMed/18722174" } ] } ], "crossref": [ { "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18722174", "url": "https://glygen.org/publication/PubMed/18722174", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "KRPRDDEEEEQKMRRKQT", "start_aa": "K", "up_seq": "MDVGELLSYQPNRGT", "down_seq": "GTRERGRYREEEMTVVEEAD", "mutagenesis": [ { "sequence_org": "KRPRDDEEEEQKMRRKQT", "sequence_mut": "", "comment": "Nuclear and cytoplasmic localization.", "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "PubMed", "id": "18722174", "url": "https://glygen.org/publication/PubMed/18722174" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8WYA6-1.14.14", "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": "Q8WYA6-1.521.563", "start_pos": 521, "end_pos": 563, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structural and mutational analysis reveals that CTNNBL1 binds NLSs in a manner distinct from that of its closest armadillo-relative, karyopherin alpha.", "journal": "FEBS letters", "date": "2014", "authors": "Ganesh K, van Maldegem F, Telerman SB, Simpson P, Johnson CM, Williams RL, Neuberger MS, Rada C", "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "reference": [ { "type": "PubMed", "id": "24269683", "url": "https://glygen.org/publication/PubMed/24269683" } ] } ], "crossref": [ { "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24269683", "url": "https://glygen.org/publication/PubMed/24269683", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "MRGSSIKIVRHIIKEYAENIGDGRSPEFRENEQKRILGLLENF", "start_aa": "M", "up_seq": "AEICNANVPQIRQRVHQILN", "down_seq": "", "mutagenesis": [ { "sequence_org": "MRGSSIKIVRHIIKEYAENIGDGRSPEFRENEQKRILGLLENF", "sequence_mut": "", "comment": "No change in NLS binding nor folding.", "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "PubMed", "id": "24269683", "url": "https://glygen.org/publication/PubMed/24269683" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q8WYA6-1.507.507", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8WYA6-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q8WYA6-1.545.545", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8WYA6-1.552.552", "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": "Q8WYA6-1.14.14", "start_pos": 14, "end_pos": 14, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2073141458", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2073141458", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2073141458", "url": "https://www.ensembl.org/id/rs2073141458", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "MDVGELLSYQPNR", "down_seq": "TKRPRDDEEEEQKMRRKQTG", "snv": [ { "evidence": [ { "id": "rs2073141458", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2073141458" }, { "id": "rs2073141458", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2073141458" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRG->NRS).", "chr_id": "20", "chr_pos": "37732888", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G14", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q8WYA6-1.16.33", "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": "Q8WYA6-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs774420988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774420988", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs774420988", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774420988", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs774420988", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774420988#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs774420988", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774420988", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs774420988", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774420988", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LYHLLVELNAVQSLLGLLGH", "down_seq": "NTDVSIAVVDLLQELTDIDT", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" }, { "id": "rs774420988", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774420988" }, { "id": "rs774420988", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs774420988" }, { "id": "rs774420988", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs774420988#frequency_tab" }, { "id": "rs774420988", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs774420988" }, { "id": "rs774420988", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs774420988" } ], "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 (DNT->NNT).", "chr_id": "20", "chr_pos": "37746598", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D153", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "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": "Q8WYA6-1.301.301", "start_pos": 301, "end_pos": 301, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200219582", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200219582", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200219582", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200219582", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GELDGIDVLLQQLSVFKRHN", "down_seq": "STAEEQEMMENLFDSLCSCL", "snv": [ { "evidence": [ { "id": "rs200219582", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200219582" }, { "id": "rs200219582", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs200219582" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "H", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NHS).", "chr_id": "20", "chr_pos": "37779206", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P301", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "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": "20", "chr_pos": "37779205", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P301", "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": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q8WYA6-1.314.314", "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": 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": "Q8WYA6-1.314.314", "start_pos": 314, "end_pos": 314, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1359762307", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359762307", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1359762307", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359762307", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "SVFKRHNPSTAEEQEMMENL", "down_seq": "DSLCSCLMLSSNRERFLKGE", "snv": [ { "evidence": [ { "id": "rs1359762307", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1359762307" }, { "id": "rs1359762307", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1359762307" } ], "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": "20", "chr_pos": "37779245", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F314", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8WYA6-1.301.301", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WYA6-1.347.347", "start_pos": 347, "end_pos": 347, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "RERFLKGEGLQLMNLMLREK", "down_seq": "ISRSSALKVLDHAMIGPEGT", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "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 (KIS->NIS).", "chr_id": "20", "chr_pos": "37802876", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K347", "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": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8WYA6-1.351.351", "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": "Q8WYA6-1.380.380", "start_pos": 380, "end_pos": 380, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AMIGPEGTDNCHKFVDILGL", "down_seq": "TIFPLFMKSPRKIKKVGTTE", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "37802973", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R380", "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": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q8WYA6-1.389.389", "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": "Q8WYA6-1.430.430", "start_pos": 430, "end_pos": 430, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs770360937", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770360937", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs770360937", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770360937", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs770360937", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770360937", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "ILASLLRNLRGQQRTRLLNK", "down_seq": "TENDSEKVDRLMELHFKYLG", "snv": [ { "evidence": [ { "id": "rs770360937", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770360937" }, { "id": "rs770360937", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs770360937" }, { "id": "rs770360937", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs770360937" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKF->NKC).", "chr_id": "20", "chr_pos": "37840177", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F430", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8WYA6-1.431.431", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WYA6-1.488.488", "start_pos": 488, "end_pos": 488, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RRGEIIDNDTEEEFYLRRLD", "down_seq": "GLFVLQHICYIMAEICNANV", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "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": "20", "chr_pos": "37859969", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A488", "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": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "upstream", "id": "Q8WYA6-1.507.507", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WYA6-1.507.507", "start_pos": 507, "end_pos": 507, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs772027227", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772027227", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs772027227", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772027227", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs772027227", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772027227#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs772027227", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772027227", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "DAGLFVLQHICYIMAEICNA", "down_seq": "VPQIRQRVHQILNMRGSSIK", "snv": [ { "evidence": [ { "id": "rs772027227", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772027227" }, { "id": "rs772027227", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs772027227" }, { "id": "rs772027227", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs772027227#frequency_tab" }, { "id": "rs772027227", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs772027227" } ], "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": "20", "chr_pos": "37860026", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N507", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8WYA6-1.488.488", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q8WYA6-1.509.509", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8WYA6-1.521.563", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8WYA6-1.522.522", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WYA6-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs760729842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760729842", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760729842", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760729842", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760729842", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760729842", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs760729842", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760729842", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GLFVLQHICYIMAEICNANV", "down_seq": "QIRQRVHQILNMRGSSIKIV", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" }, { "id": "rs760729842", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760729842" }, { "id": "rs760729842", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760729842" }, { "id": "rs760729842", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760729842" }, { "id": "rs760729842", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs760729842" } ], "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 (NVP->NVS).", "chr_id": "20", "chr_pos": "37860031", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P509", "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q8WYA6-1.507.507", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8WYA6-1.521.563", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8WYA6-1.522.522", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WYA6-1.522.522", "start_pos": 522, "end_pos": 522, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EICNANVPQIRQRVHQILNM", "down_seq": "GSSIKIVRHIIKEYAENIGD", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "20", "chr_pos": "37860305", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R522", "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": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8WYA6-1.507.507", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q8WYA6-1.509.509", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8WYA6-1.552.552", "start_pos": 552, "end_pos": 552, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "IIKEYAENIGDGRSPEFREN", "down_seq": "QKRILGLLENF", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "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 (3).", "chr_id": "20", "chr_pos": "37871975", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E552", "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" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8WYA6-1.521.563", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8WYA6-1.545.545", "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": "Q8WYA6-1.91.91", "start_pos": 91, "end_pos": 91, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8WYA6", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EEEEEPLDESSVKKMILTFE", "down_seq": "RSYKNQELRIKFPDNPEKFM", "snv": [ { "evidence": [ { "id": "Q8WYA6", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8WYA6" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KRS->NRS).", "chr_id": "20", "chr_pos": "37737431", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "K91", "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": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "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": "Q8WYA6-1.351.351", "start_pos": 351, "end_pos": 351, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "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": "Q8WYA6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6", "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": "LKGEGLQLMNLMLREKKISR", "down_seq": "SALKVLDHAMIGPEGTDNCH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser351" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8WYA6-1.347.347", "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": "Q8WYA6-1.389.389", "start_pos": 389, "end_pos": 389, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "iPTMnet", "id": "Q8WYA6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "NCHKFVDILGLRTIFPLFMK", "down_seq": "PRKIKKVGTTEKEHEEHVCS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6" } ], "site_lbl": "Ser389" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8WYA6-1.380.380", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q8WYA6-1.409.409", "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": "Q8WYA6-1.545.545", "start_pos": 545, "end_pos": 545, "uniprot_canonical_ac": "Q8WYA6-1", "length": 563, "uniprot_id": "CTBL1_HUMAN", "protein_name": "Beta-catenin-like protein 1", "refseq_ac": "NP_001268424", "refseq_name": "beta-catenin-like protein 1 isoform 2", "gene_name": "CTNNBL1", "gene_names_uniprotkb": "CTNNBL1; C20orf33; PP8304", "gene_names_refseq": "C20orf33; CTNNBL1; IMD99; NAP; P14L; PP8304; dJ633O20.1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "iPTMnet", "id": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6" } ], "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": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "database": "iPTMnet", "id": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6" } ], "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": "Q8WYA6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "Q8WYA6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q8WYA6-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6", "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": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "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": "SIKIVRHIIKEYAENIGDGR", "down_seq": "PEFRENEQKRILGLLENF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8WYA6", "url": "https://www.uniprot.org/uniprotkb/Q8WYA6" }, { "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": "Q8WYA6", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8WYA6" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser545" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "409", "end_pos": "409" }, { "start_pos": "431", "end_pos": "431" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "16", "end_pos": "33" }, { "start_pos": "521", "end_pos": "563" } ] }, { "type": "snv", "site_list": [ { "start_pos": "14", "end_pos": "14" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "301", "end_pos": "301" }, { "start_pos": "314", "end_pos": "314" }, { "start_pos": "347", "end_pos": "347" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "409", "end_pos": "409" }, { "start_pos": "430", "end_pos": "430" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "488", "end_pos": "488" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "552", "end_pos": "552" }, { "start_pos": "91", "end_pos": "91" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "351", "end_pos": "351" }, { "start_pos": "389", "end_pos": "389" }, { "start_pos": "545", "end_pos": "545" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q8WYA6-1.521.563", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8WYA6-1.552.552", "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": "Q49A88-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "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": "Q49A88", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q49A88" } ], "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": "Q49A88", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q49A88", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PKVHSEVQTDGNSQFASQGK", "down_seq": "VSATCTDVLRNSFNTSPGVP", "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": "Thr292", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q49A88", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q49A88" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q49A88-1.294.294", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q49A88-1.294.294", "start_pos": 294, "end_pos": 294, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "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": "Q49A88", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q49A88" } ], "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": "Q49A88", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q49A88", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VHSEVQTDGNSQFASQGKTV", "down_seq": "ATCTDVLRNSFNTSPGVPCS", "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": "Ser294", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q49A88", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q49A88" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q49A88-1.292.292", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q49A88-1.640.640", "start_pos": 640, "end_pos": 640, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2034630034", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034630034", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2034630034", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034630034#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QILGITLRQRDAEVTRLREL", "down_seq": "RTLQTSMAKLLSDLSVDSAR", "snv": [ { "evidence": [ { "id": "rs2034630034", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2034630034" }, { "id": "rs2034630034", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs2034630034#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 (TRT->NRT).", "chr_id": "3", "chr_pos": "123915578", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T640", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "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": "Q49A88-1.878.878", "start_pos": 878, "end_pos": 878, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q49A88", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q49A88", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KKIKEAIGKIPAATKEPEEQ", "down_seq": "ACHGPSGCLSNSLQVKGNTV", "snv": [ { "evidence": [ { "id": "Q49A88", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q49A88" } ], "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": "3", "chr_pos": "123914885", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T878", "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": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "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": "Q49A88-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "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": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVHGLDGCASLLRDILRNED", "down_seq": "GSETAYLENRSNSRPLESKR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "site_lbl": "Ser124" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "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": "Q49A88-1.670.670", "start_pos": 670, "end_pos": 670, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "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": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LLSDLSVDSARCKPGNNLTK", "down_seq": "LLNIHDKQLQHDPAPAHTSI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "site_lbl": "Ser670" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "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": "Q49A88-1.754.754", "start_pos": 754, "end_pos": 754, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "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": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QNSNTRGMEEASAPGIISAL", "down_seq": "KQDSDEGSETMALIEDEHNL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "site_lbl": "Ser754" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "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": "Q49A88-1.798.798", "start_pos": 798, "end_pos": 798, "uniprot_canonical_ac": "Q49A88-1", "length": 953, "uniprot_id": "CCD14_HUMAN", "protein_name": "Coiled-coil domain-containing protein 14", "refseq_ac": "NP_001295246", "refseq_name": "coiled-coil domain-containing protein 14 isoform 2", "gene_name": "CCDC14", "gene_names_uniprotkb": "CCDC14", "gene_names_refseq": "CCDC14", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" } ], "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": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IYIPFARSTPEKKSPLSKRL", "down_seq": "PQPQIRAATTQLVSNSGLAV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q49A88", "url": "https://www.uniprot.org/uniprotkb/Q49A88" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q49A88", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q49A88" } ], "site_lbl": "Ser798" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "292", "end_pos": "292" }, { "start_pos": "294", "end_pos": "294" } ] }, { "type": "snv", "site_list": [ { "start_pos": "640", "end_pos": "640" }, { "start_pos": "878", "end_pos": "878" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "670", "end_pos": "670" }, { "start_pos": "754", "end_pos": "754" }, { "start_pos": "798", "end_pos": "798" } ] } ], "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": "P61601-1.73.73", "start_pos": 73, "end_pos": 73, "uniprot_canonical_ac": "P61601-1", "length": 193, "uniprot_id": "NCALD_HUMAN", "protein_name": "Neurocalcin-delta", "refseq_ac": "NP_001035714", "refseq_name": "neurocalcin-delta", "gene_name": "NCALD", "gene_names_uniprotkb": "NCALD", "gene_names_refseq": "NCALD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P61601", "url": "https://www.uniprot.org/uniprotkb/P61601" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P61601", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P61601", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GNFFPYGDASKFAEHVFRTF", "down_seq": "ANGDGTIDFREFIIALSVTS", "snv": [ { "evidence": [ { "id": "P61601", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P61601" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "8", "chr_pos": "101719413", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D73", "disease": [ { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "73", "end_pos": "73" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "165", "end_pos": "165" } ] } ], "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": "P61601-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P61601-1", "length": 193, "uniprot_id": "NCALD_HUMAN", "protein_name": "Neurocalcin-delta", "refseq_ac": "NP_001035714", "refseq_name": "neurocalcin-delta", "gene_name": "NCALD", "gene_names_uniprotkb": "NCALD", "gene_names_refseq": "NCALD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P61601", "url": "https://www.uniprot.org/uniprotkb/P61601" } ], "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": "P61601", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P61601" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "P61601", "url": "https://www.iedb.org/epitope/P61601", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P61601", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P61601", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DLDGNGYISKAEMLEIVQAI", "down_seq": "KMVSSVMKMPEDESTPEKRT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "IEDB", "id": "P61601", "url": "https://www.iedb.org/epitope/P61601" }, { "database": "iPTMnet", "id": "P61601", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P61601" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Tyr129" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "73", "end_pos": "73" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "165", "end_pos": "165" } ] } ], "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": "P61601-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "P61601-1", "length": 193, "uniprot_id": "NCALD_HUMAN", "protein_name": "Neurocalcin-delta", "refseq_ac": "NP_001035714", "refseq_name": "neurocalcin-delta", "gene_name": "NCALD", "gene_names_uniprotkb": "NCALD", "gene_names_refseq": "NCALD", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P61601", "url": "https://www.uniprot.org/uniprotkb/P61601" } ], "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": "P61601", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P61601" } ], "reference": [ { "type": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ] } ], "crossref": [ { "id": "P61601", "url": "https://www.iedb.org/epitope/P61601", "database": "IEDB", "categories": [ "Other" ] }, { "id": "P61601", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P61601", "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": "PEKRTEKIFRQMDTNRDGKL", "down_seq": "LEEFIRGAKSDPSIVRLLQC", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "IEDB", "id": "P61601", "url": "https://www.iedb.org/epitope/P61601" }, { "database": "iPTMnet", "id": "P61601", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P61601" }, { "database": "PubMed", "id": "35494241", "url": "https://glygen.org/publication/PubMed/35494241" } ], "site_lbl": "Ser165" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "73", "end_pos": "73" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "129", "end_pos": "129" }, { "start_pos": "165", "end_pos": "165" } ] } ], "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": "Q8NHH9-1.308.308", "start_pos": 308, "end_pos": 308, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "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": "Q8NHH9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHH9" } ], "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": "Q8NHH9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHH9" } ], "reference": [ { "type": "PubMed", "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422" } ] }, { "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": "Q8NHH9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHH9" }, { "database": "O-GlcNAc Atlas", "id": "Q8NHH9", "url": "https://oglcnac.org/atlas/detail/Q8NHH9" } ], "reference": [ { "type": "PubMed", "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160" } ] }, { "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": "Q8NHH9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHH9" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] } ], "crossref": [ { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHH9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHH9", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "40914422", "url": "https://glygen.org/publication/PubMed/40914422", "database": "PubMed", "categories": [ "Other" ] }, { "id": "25367160", "url": "https://glygen.org/publication/PubMed/25367160", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHH9", "url": "https://oglcnac.org/atlas/detail/Q8NHH9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs746341011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746341011", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs746341011", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746341011", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs746341011", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746341011#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs746341011", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746341011", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs776696907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776696907", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776696907", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776696907", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776696907", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776696907#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs776696907", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776696907", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FSNLGCFLLPHPGLKVATNP", "down_seq": "FDGRLKDIDEDFKRELRNLV", "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": "Ser308", "evidence": [ { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "Q8NHH9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q8NHH9" }, { "id": "40914422", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40914422" }, { "id": "25367160", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/25367160" }, { "id": "34725712", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34725712" }, { "id": "Q8NHH9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q8NHH9" } ] } ], "snv": [ { "evidence": [ { "id": "rs746341011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746341011" }, { "id": "rs746341011", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746341011" }, { "id": "rs746341011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746341011#frequency_tab" }, { "id": "rs746341011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746341011" } ], "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": "38310330", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S308", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs776696907", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776696907" }, { "id": "rs776696907", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776696907" }, { "id": "rs776696907", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs776696907#frequency_tab" }, { "id": "rs776696907", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776696907" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->N).", "chr_id": "2", "chr_pos": "38310329", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S308", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs746341011", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746341011" }, { "id": "rs746341011", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs746341011" }, { "id": "rs746341011", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs746341011#frequency_tab" }, { "id": "rs746341011", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs746341011" } ], "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": "2", "chr_pos": "38310330", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S308", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NHH9-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q8NHH9-1.307.307", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q8NHH9-1.107.107", "start_pos": 107, "end_pos": 107, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Atlastin GTPases are required for Golgi apparatus and ER morphogenesis.", "journal": "Human molecular genetics", "date": "2008", "authors": "Rismanchi N, Soderblom C, Stadler J, Zhu PP, Blackstone C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "18270207", "url": "https://glygen.org/publication/PubMed/18270207" } ] }, { "title": "Cooperation of the ER-shaping proteins atlastin, lunapark, and reticulons to generate a tubular membrane network.", "journal": "eLife", "date": "2016", "authors": "Wang S, Tukachinsky H, Romano FB, Rapoport TA", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "reference": [ { "type": "PubMed", "id": "27619977", "url": "https://glygen.org/publication/PubMed/27619977" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18270207", "url": "https://glygen.org/publication/PubMed/18270207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "27619977", "url": "https://glygen.org/publication/PubMed/27619977", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "EHIRDLNIVVVSVAGAFRKG", "down_seq": "SFLLDFMLRYMYNKDSQSWI", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Alters endoplasmic reticulum morphology.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "18270207", "url": "https://glygen.org/publication/PubMed/18270207" }, { "database": "PubMed", "id": "27619977", "url": "https://glygen.org/publication/PubMed/27619977" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "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": "Q8NHH9-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Atlastin GTPases are required for Golgi apparatus and ER morphogenesis.", "journal": "Human molecular genetics", "date": "2008", "authors": "Rismanchi N, Soderblom C, Stadler J, Zhu PP, Blackstone C", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "18270207", "url": "https://glygen.org/publication/PubMed/18270207" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18270207", "url": "https://glygen.org/publication/PubMed/18270207", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GRLAMEEIYQKPFQTLMFLI", "down_seq": "DWSYPYEHSYGLEGGKQFLE", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "Q", "comment": "Alters endoplasmic reticulum morphogenesis.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "18270207", "url": "https://glygen.org/publication/PubMed/18270207" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "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": "Q8NHH9-1.372.372", "start_pos": 372, "end_pos": 372, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LVEYFKAYIKIYQGEELPHP", "down_seq": "SMLQATAEANNLAAVAGARD", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "E", "comment": "No effect on GTP-binding or GTPase activity. Loss of function in endoplasmic reticulum tubular network membrane organization. No effect on function in endoplasmic reticulum tubular network membrane organization; when associated with R-380.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q8NHH9-1.380.380", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHH9-1.384.384", "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": "Q8NHH9-1.380.380", "start_pos": 380, "end_pos": 380, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "IKIYQGEELPHPKSMLQATA", "down_seq": "ANNLAAVAGARDTYCKSMEQ", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Loss of function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] }, { "sequence_org": "E", "sequence_mut": "R", "comment": "No effect on GTP-binding or GTPase activity. Loss of function in endoplasmic reticulum tubular network membrane organization. No effect on function in endoplasmic reticulum tubular network membrane organization; when associated with E-372.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q8NHH9-1.372.372", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHH9-1.384.384", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHH9-1.393.393", "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": "Q8NHH9-1.384.384", "start_pos": 384, "end_pos": 384, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "QGEELPHPKSMLQATAEANN", "down_seq": "AAVAGARDTYCKSMEQVCGG", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Loss of function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q8NHH9-1.372.372", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHH9-1.380.380", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHH9-1.393.393", "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": "Q8NHH9-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSDLERKHLDLKEVAIKQFR", "down_seq": "VKKMGGDEFCRRYQDQLEAE", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No effect on function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q8NHH9-1.435.435", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHH9-1.440.440", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q8NHH9-1.444.444", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHH9-1.447.447", "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": "Q8NHH9-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "ERKHLDLKEVAIKQFRSVKK", "down_seq": "GGDEFCRRYQDQLEAEIEET", "mutagenesis": [ { "sequence_org": "M", "sequence_mut": "A", "comment": "Loss of function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHH9-1.431.431", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q8NHH9-1.440.440", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q8NHH9-1.444.444", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q8NHH9-1.447.447", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q8NHH9-1.454.454", "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": "Q8NHH9-1.440.440", "start_pos": 440, "end_pos": 440, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "DLKEVAIKQFRSVKKMGGDE", "down_seq": "CRRYQDQLEAEIEETYANFI", "mutagenesis": [ { "sequence_org": "F", "sequence_mut": "A", "comment": "Decreased function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q8NHH9-1.431.431", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q8NHH9-1.435.435", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHH9-1.444.444", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHH9-1.447.447", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q8NHH9-1.454.454", "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": "Q8NHH9-1.444.444", "start_pos": 444, "end_pos": 444, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VAIKQFRSVKKMGGDEFCRR", "down_seq": "QDQLEAEIEETYANFIKHND", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "A", "comment": "No effect on function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHH9-1.431.431", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHH9-1.435.435", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q8NHH9-1.440.440", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHH9-1.447.447", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q8NHH9-1.454.454", "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": "Q8NHH9-1.447.447", "start_pos": 447, "end_pos": 447, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "KQFRSVKKMGGDEFCRRYQD", "down_seq": "LEAEIEETYANFIKHNDGKN", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "No effect on function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q8NHH9-1.431.431", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q8NHH9-1.435.435", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHH9-1.440.440", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHH9-1.444.444", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q8NHH9-1.454.454", "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": "Q8NHH9-1.454.454", "start_pos": 454, "end_pos": 454, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "An intramolecular salt bridge drives the soluble domain of GTP-bound atlastin into the postfusion conformation.", "journal": "The Journal of cell biology", "date": "2011", "authors": "Morin-Leisk J, Saini SG, Meng X, Makhov AM, Zhang P, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "KMGGDEFCRRYQDQLEAEIE", "down_seq": "TYANFIKHNDGKNIFYAART", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "A", "comment": "Loss of function in endoplasmic reticulum tubular network membrane organization.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "22065636", "url": "https://glygen.org/publication/PubMed/22065636" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q8NHH9-1.435.435", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q8NHH9-1.440.440", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q8NHH9-1.444.444", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q8NHH9-1.447.447", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHH9-1.469.469", "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": "Q8NHH9-1.555.555", "start_pos": 555, "end_pos": 555, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Reconstitution of human atlastin fusion activity reveals autoinhibition by the C terminus.", "journal": "The Journal of cell biology", "date": "2022", "authors": "Crosby D, Mikolaj MR, Nyenhuis SB, Bryce S, Hinshaw JE, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DQIAETLWEQVLKPLGDNLM", "down_seq": "ENIRQSVTNSIKAGLTDQVS", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Increased GTPase-dependent fusogenic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q8NHH9-1.556.556", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q8NHH9-1.559.559", "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": "Q8NHH9-1.556.556", "start_pos": 556, "end_pos": 556, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Reconstitution of human atlastin fusion activity reveals autoinhibition by the C terminus.", "journal": "The Journal of cell biology", "date": "2022", "authors": "Crosby D, Mikolaj MR, Nyenhuis SB, Bryce S, Hinshaw JE, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QIAETLWEQVLKPLGDNLME", "down_seq": "NIRQSVTNSIKAGLTDQVSH", "mutagenesis": [ { "sequence_org": "E", "sequence_mut": "K", "comment": "Increased GTPase-dependent fusogenic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q8NHH9-1.555.555", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q8NHH9-1.559.559", "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": "Q8NHH9-1.559.559", "start_pos": 559, "end_pos": 559, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Reconstitution of human atlastin fusion activity reveals autoinhibition by the C terminus.", "journal": "The Journal of cell biology", "date": "2022", "authors": "Crosby D, Mikolaj MR, Nyenhuis SB, Bryce S, Hinshaw JE, Lee TH", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "RefSeq", "id": "NP_001129145", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_001129145" } ], "reference": [ { "type": "PubMed", "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q8NHH9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ETLWEQVLKPLGDNLMEENI", "down_seq": "QSVTNSIKAGLTDQVSHHAR", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "E", "comment": "Increased GTPase-dependent fusogenic activity.", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "34817557", "url": "https://glygen.org/publication/PubMed/34817557" } ] } ], "snv": [ { "evidence": [ { "id": "Q8NHH9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIR->NIS).", "chr_id": "2", "chr_pos": "38296069", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R559", "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": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "mutagenesis_flag", "snv_flag" ], "glycosylation": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q8NHH9-1.555.555", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q8NHH9-1.556.556", "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": "Q8NHH9-1.18.18", "start_pos": 18, "end_pos": 18, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHH9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "MAEGDEAARGQQPHQGL", "down_seq": "RRRRTSDPSAAVNHVSSTTS", "snv": [ { "evidence": [ { "id": "Q8NHH9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "W", "sequence_mut": "R", "comment": "Somatic mutation passed 2 filters: patient freq. (1.1%); num. of cancers (3).", "chr_id": "2", "chr_pos": "38377209", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "W18", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "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: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" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q8NHH9-1.24.24", "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": "Q8NHH9-1.285.285", "start_pos": 285, "end_pos": 285, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373365211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373365211", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373365211", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373365211", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373365211", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373365211#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373365211", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373365211", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "KRLQVKQNQHEELQNVRKHI", "down_seq": "NCFSNLGCFLLPHPGLKVAT", "snv": [ { "evidence": [ { "id": "rs373365211", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373365211" }, { "id": "rs373365211", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373365211" }, { "id": "rs373365211", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373365211#frequency_tab" }, { "id": "rs373365211", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373365211" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "H", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (HNC->NNC).", "chr_id": "2", "chr_pos": "38310399", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "H285", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q8NHH9-1.292.292", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHH9-1.292.292", "start_pos": 292, "end_pos": 292, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1667687645", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1667687645", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1667687645", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1667687645#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "NQHEELQNVRKHIHNCFSNL", "down_seq": "CFLLPHPGLKVATNPSFDGR", "snv": [ { "evidence": [ { "id": "rs1667687645", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1667687645" }, { "id": "rs1667687645", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1667687645#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLG->NLS).", "chr_id": "2", "chr_pos": "38310378", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G292", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q8NHH9-1.285.285", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q8NHH9-1.307.307", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q8NHH9-1.308.308", "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": "Q8NHH9-1.307.307", "start_pos": 307, "end_pos": 307, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHH9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs765093782", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765093782", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs765093782", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765093782", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs765093782", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765093782", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs150956803", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150956803", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs150956803", "url": "https://www.ensembl.org/id/rs150956803", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs150956803", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150956803", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "CFSNLGCFLLPHPGLKVATN", "down_seq": "SFDGRLKDIDEDFKRELRNL", "snv": [ { "evidence": [ { "id": "Q8NHH9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2053", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NHS).", "chr_id": "2", "chr_pos": "38310332", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P307", "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": "rs765093782", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765093782" }, { "id": "rs765093782", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs765093782" }, { "id": "rs765093782", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs765093782" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NRS).", "chr_id": "2", "chr_pos": "38310332", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P307", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q8NHH9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9" }, { "id": "rs150956803", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs150956803" }, { "id": "rs150956803", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs150956803" }, { "id": "rs150956803", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs150956803" } ], "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": "2", "chr_pos": "38310333", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P307", "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": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHH9-1.292.292", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q8NHH9-1.308.308", "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": 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": "Q8NHH9-1.343.343", "start_pos": 343, "end_pos": 343, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1171304048", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171304048", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1171304048", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1171304048#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1171304048", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171304048", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELRNLVPLLLAPENLVEKEI", "down_seq": "GSKVTCRDLVEYFKAYIKIY", "snv": [ { "evidence": [ { "id": "rs1171304048", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1171304048" }, { "id": "rs1171304048", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1171304048#frequency_tab" }, { "id": "rs1171304048", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1171304048" } ], "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": "2", "chr_pos": "38309422", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S343", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "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": "Q8NHH9-1.393.393", "start_pos": 393, "end_pos": 393, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs61734830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734830", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61734830", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61734830", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61734830", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734830", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61734830", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61734830#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61734830", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61734830", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SMLQATAEANNLAAVAGARD", "down_seq": "YCKSMEQVCGGDKPYIAPSD", "snv": [ { "evidence": [ { "id": "rs61734830", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734830" }, { "id": "rs61734830", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61734830" }, { "id": "rs61734830", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61734830" }, { "id": "rs61734830", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61734830#frequency_tab" }, { "id": "rs61734830", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61734830" } ], "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 (TYC->NYC).", "chr_id": "2", "chr_pos": "38299278", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0.00137363", "site_lbl": "T393", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q8NHH9-1.380.380", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q8NHH9-1.384.384", "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": "Q8NHH9-1.469.469", "start_pos": 469, "end_pos": 469, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs74573857", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74573857", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs74573857", "url": "https://www.ensembl.org/id/rs74573857", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "EAEIEETYANFIKHNDGKNI", "down_seq": "YAARTPATLFAVMFAMYIIS", "snv": [ { "evidence": [ { "id": "rs74573857", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs74573857" }, { "id": "rs74573857", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs74573857" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NIF->NIC).", "chr_id": "2", "chr_pos": "38298370", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F469", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q8NHH9-1.454.454", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q8NHH9-1.480.480", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHH9-1.480.480", "start_pos": 480, "end_pos": 480, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q8NHH9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "IKHNDGKNIFYAARTPATLF", "down_seq": "VMFAMYIISGLTGFIGLNSI", "snv": [ { "evidence": [ { "id": "Q8NHH9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8NHH9" } ], "glycoeffect": [], "subjects_tested": "606", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "2", "chr_pos": "38298337", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A480", "disease": [ { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID: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": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q8NHH9-1.469.469", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q8NHH9-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "Q8NHH9-1", "length": 583, "uniprot_id": "ATLA2_HUMAN", "protein_name": "Atlastin-2", "refseq_ac": "NP_001129145", "refseq_name": "atlastin-2 isoform 2", "gene_name": "ATL2", "gene_names_uniprotkb": "ATL2; ARL6IP2", "gene_names_refseq": "ARL3IP2; ARL6IP2; ATL-2; ATL2; aip-2; atlastin2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" } ], "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": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "iPTMnet", "id": "Q8NHH9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHH9" } ], "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": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "iPTMnet", "id": "Q8NHH9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHH9" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "Q8NHH9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHH9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GDEAARGQQPHQGLWRRRRT", "down_seq": "DPSAAVNHVSSTTSLGENYE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q8NHH9", "url": "https://www.uniprot.org/uniprotkb/Q8NHH9" }, { "database": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q8NHH9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q8NHH9" } ], "site_lbl": "Ser24" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "308", "end_pos": "308" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "107", "end_pos": "107" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "372", "end_pos": "372" }, { "start_pos": "380", "end_pos": "380" }, { "start_pos": "384", "end_pos": "384" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "444", "end_pos": "444" }, { "start_pos": "447", "end_pos": "447" }, { "start_pos": "454", "end_pos": "454" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "556", "end_pos": "556" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "snv", "site_list": [ { "start_pos": "18", "end_pos": "18" }, { "start_pos": "285", "end_pos": "285" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": "308", "end_pos": "308" }, { "start_pos": "343", "end_pos": "343" }, { "start_pos": "393", "end_pos": "393" }, { "start_pos": "469", "end_pos": "469" }, { "start_pos": "480", "end_pos": "480" }, { "start_pos": "559", "end_pos": "559" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "24", "end_pos": "24" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q8NHH9-1.18.18", "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": "Q9NVP2-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "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": "Q9NVP2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] } ], "crossref": [ { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NVP2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NVP2", "database": "O-GlcNAc Database", "categories": [ "Other" ] } ], "glycosylation": [ { "glytoucan_ac": "G49108TO", "type": "O-linked", "subtype": "O-GlcNAcylation", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "evidence": [ { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "id": "Q9NVP2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9NVP2" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "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": "Q9NVP2-1.169.169", "start_pos": 169, "end_pos": 169, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry.", "journal": "Nature communications", "date": "2022", "authors": "Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069" } ] } ], "crossref": [ { "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FHINWDNNMDRLEAIETQDP", "down_seq": "LGCGLPLNCTPIKGLGLPGC", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "No apparent effect on ASF1B phosphorylation by TLK2. Reduced phosphorylation of ASF1B by TLK2 when associated with A-198.", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "PubMed", "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q9NVP2-1.179.179", "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": "Q9NVP2-1.198.198", "start_pos": 198, "end_pos": 198, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Tousled-like kinase 2 targets ASF1 histone chaperones through client mimicry.", "journal": "Nature communications", "date": "2022", "authors": "Simon B, Lou HJ, Huet-Calderwood C, Shi G, Boggon TJ, Turk BE, Calderwood DA", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069" } ] }, { "title": "Phosphorylation-mediated control of histone chaperone ASF1 levels by Tousled-like kinases.", "journal": "PloS one", "date": "2009", "authors": "Pilyugin M, Demmers J, Verrijzer CP, Karch F, Moshkin YM", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "20016786", "url": "https://glygen.org/publication/PubMed/20016786" } ] }, { "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": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "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": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20016786", "url": "https://glygen.org/publication/PubMed/20016786", "database": "PubMed", "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": "CTPIKGLGLPGCIPGLLPEN", "down_seq": "MDCI", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Reduced phosphorylation of ASF1B by TLK2 when associated with A-169.", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "PubMed", "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q86UE8-1", "kinase_gene_name": "TLK2", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" }, { "database": "PubMed", "id": "20016786", "url": "https://glygen.org/publication/PubMed/20016786" } ], "site_lbl": "Ser198" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; by TLK2", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "35136069", "url": "https://glygen.org/publication/PubMed/35136069" }, { "database": "PubMed", "id": "20016786", "url": "https://glygen.org/publication/PubMed/20016786" } ], "site_lbl": "Ser198" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9NVP2-1.179.179", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9NVP2-1.36.36", "start_pos": 36, "end_pos": 36, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply.", "journal": "The EMBO journal", "date": "2012", "authors": "Ask K, Jasencakova Z, Menard P, Feng Y, Almouzni G, Groth A", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "22407294", "url": "https://glygen.org/publication/PubMed/22407294" } ] } ], "crossref": [ { "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22407294", "url": "https://glygen.org/publication/PubMed/22407294", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SPFHSPFRFEISFECSEALA", "down_seq": "DLEWKIIYVGSAESEEFDQI", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolishes CDAN1 interaction.", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "PubMed", "id": "22407294", "url": "https://glygen.org/publication/PubMed/22407294" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9NVP2-1.37.37", "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": "Q9NVP2-1.37.37", "start_pos": 37, "end_pos": 37, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Codanin-1, mutated in the anaemic disease CDAI, regulates Asf1 function in S-phase histone supply.", "journal": "The EMBO journal", "date": "2012", "authors": "Ask K, Jasencakova Z, Menard P, Feng Y, Almouzni G, Groth A", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "22407294", "url": "https://glygen.org/publication/PubMed/22407294" } ] } ], "crossref": [ { "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "22407294", "url": "https://glygen.org/publication/PubMed/22407294", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PFHSPFRFEISFECSEALAD", "down_seq": "LEWKIIYVGSAESEEFDQIL", "mutagenesis": [ { "sequence_org": "D", "sequence_mut": "A", "comment": "Abolishes CDAN1 interaction.", "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" }, { "database": "PubMed", "id": "22407294", "url": "https://glygen.org/publication/PubMed/22407294" } ] } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9NVP2-1.36.36", "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": "Q9NVP2-1.142.142", "start_pos": 142, "end_pos": 142, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "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": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2", "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": "LRENPPMKPDFSQLQRNILA", "down_seq": "NPRVTRFHINWDNNMDRLEA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Ser142" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "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": "Q9NVP2-1.179.179", "start_pos": 179, "end_pos": 179, "uniprot_canonical_ac": "Q9NVP2-1", "length": 202, "uniprot_id": "ASF1B_HUMAN", "protein_name": "Histone chaperone ASF1B", "refseq_ac": "NP_060624", "refseq_name": "histone chaperone ASF1B", "gene_name": "ASF1B", "gene_names_uniprotkb": "ASF1B", "gene_names_refseq": "ASF1B; CIA-II", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9NVP2", "url": "https://www.uniprot.org/uniprotkb/Q9NVP2" } ], "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": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2", "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": "RLEAIETQDPSLGCGLPLNC", "down_seq": "PIKGLGLPGCIPGLLPENSM", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9NVP2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9NVP2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr179" } ], "all_sites": [ { "type": "mutagenesis", "site_list": [ { "start_pos": "169", "end_pos": "169" }, { "start_pos": "198", "end_pos": "198" }, { "start_pos": "36", "end_pos": "36" }, { "start_pos": "37", "end_pos": "37" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "142", "end_pos": "142" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "198", "end_pos": "198" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9NVP2-1.169.169", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9NVP2-1.198.198", "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": "Q68CZ2-1.1050.1050", "start_pos": 1050, "end_pos": 1050, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "rs61731308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61731308", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs61731308", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61731308", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs61731308", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61731308", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs61731308", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61731308#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs61731308", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61731308", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GLPPEEDLGALLANSHGASP", "down_seq": "PSIPLTATGAADNGFLSHNF", "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": "Thr1050", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs61731308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61731308" }, { "id": "rs61731308", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61731308" }, { "id": "rs61731308", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61731308" }, { "id": "rs61731308", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61731308#frequency_tab" }, { "id": "rs61731308", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61731308" } ], "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": "7", "chr_pos": "47303259", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "0.0174647", "site_lbl": "T1050", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->N).", "chr_id": "7", "chr_pos": "47303258", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T1050", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs61731308", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61731308" }, { "id": "rs61731308", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs61731308" }, { "id": "rs61731308", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs61731308" }, { "id": "rs61731308", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs61731308#frequency_tab" }, { "id": "rs61731308", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs61731308" } ], "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": "7", "chr_pos": "47303259", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "0.0174647", "site_lbl": "T1050", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl", "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": "Q68CZ2-1.1118.1118", "start_pos": 1118, "end_pos": 1118, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q68CZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2" }, { "database": "O-GlcNAc Atlas", "id": "Q68CZ2", "url": "https://oglcnac.org/atlas/detail/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "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": "Q68CZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "Q68CZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "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": "Q68CZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2", "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": "39302247", "url": "https://glygen.org/publication/PubMed/39302247", "database": "PubMed", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "https://oglcnac.org/atlas/detail/Q68CZ2", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs766860708", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766860708", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs766860708", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766860708", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs766860708", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766860708", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1021535350", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021535350", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1021535350", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1021535350#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1021535350", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021535350", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPEKKRASEGDRSLGSVSPS", "down_seq": "SGFSSPHSGSTISIPFPNVL", "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": "Ser1118", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q68CZ2", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q68CZ2" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "39302247", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39302247" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "Q68CZ2", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q68CZ2" } ] } ], "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "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": "7", "chr_pos": "47303054", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S1118", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs766860708", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766860708" }, { "id": "rs766860708", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs766860708" }, { "id": "rs766860708", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs766860708" } ], "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": "7", "chr_pos": "47303363", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1118", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1021535350", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1021535350" }, { "id": "rs1021535350", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1021535350#frequency_tab" }, { "id": "rs1021535350", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1021535350" } ], "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": "7", "chr_pos": "47303362", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1118", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q68CZ2-1.1108.1108", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.1129.1129", "categories": [ "glycosylation_flag", "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment", "start_aa", "end_aa", "residue", "site_lbl" ] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.1129.1129", "start_pos": 1129, "end_pos": 1129, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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 Atlas", "id": "Q68CZ2", "url": "https://oglcnac.org/atlas/detail/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://oglcnac.org/atlas/detail/Q68CZ2", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs747369771", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747369771", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747369771", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747369771", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747369771", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747369771", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs548297522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548297522", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs548297522", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548297522", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs548297522", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548297522", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs548297522", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548297522#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs548297522", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548297522", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RSLGSVSPSSSGFSSPHSGS", "down_seq": "ISIPFPNVLPDFSKASEAAS", "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": "Thr1129", "evidence": [ { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "Q68CZ2", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q68CZ2" } ] } ], "snv": [ { "evidence": [ { "id": "rs747369771", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747369771" }, { "id": "rs747369771", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747369771" }, { "id": "rs747369771", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747369771" } ], "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": "7", "chr_pos": "47303022", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1129", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs548297522", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548297522" }, { "id": "rs548297522", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs548297522" }, { "id": "rs548297522", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs548297522" }, { "id": "rs548297522", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs548297522#frequency_tab" }, { "id": "rs548297522", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs548297522" } ], "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": "47303021", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "0.000196232", "site_lbl": "T1129", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.1118.1118", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68CZ2-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q68CZ2-1.1149.1149", "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": 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": "Q68CZ2-1.573.573", "start_pos": 573, "end_pos": 573, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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 Atlas", "id": "Q68CZ2", "url": "https://oglcnac.org/atlas/detail/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://oglcnac.org/atlas/detail/Q68CZ2", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1325918013", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1325918013", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1325918013", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1325918013#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1325918013", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1325918013", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RTFGSREPKQPQPLLRKPSV", "down_seq": "AQMQAYGQSSYSTQTWVRQQ", "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": "Ser573", "evidence": [ { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "Q68CZ2", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q68CZ2" } ] } ], "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" }, { "id": "rs1325918013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1325918013" }, { "id": "rs1325918013", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1325918013#frequency_tab" }, { "id": "rs1325918013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1325918013" } ], "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": "7", "chr_pos": "47368928", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S573", "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": "rs1325918013", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1325918013" }, { "id": "rs1325918013", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1325918013#frequency_tab" }, { "id": "rs1325918013", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1325918013" } ], "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": "7", "chr_pos": "47368928", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S573", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q68CZ2-1.553.553", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68CZ2-1.571.571", "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": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.1173.1173", "start_pos": 1173, "end_pos": 1173, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PEAK1 Y635 phosphorylation regulates cell migration through association with Tensin3 and integrins.", "journal": "The Journal of cell biology", "date": "2022", "authors": "Zuidema A, Atherton P, Kreft M, Hoekman L, Bleijerveld OB, Nagaraj N, Chen N, Fassler R, Sonnenberg A", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "RefSeq", "id": "NP_073585", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_073585" } ], "reference": [ { "type": "PubMed", "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021" } ] }, { "title": "The Tensin-3 protein, including its SH2 domain, is phosphorylated by Src and contributes to tumorigenesis and metastasis.", "journal": "Cancer cell", "date": "2009", "authors": "Qian X, Li G, Vass WC, Papageorge A, Walker RC, Asnaghi L, Steinbach PJ, Tosato G, Hunter K, Lowy DR", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DSPGDKLVIVKFVQDTSKFW", "down_seq": "KADISREQAIAMLKDKEPGS", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Significantly reduced interaction with PEAK1; when associated with F-1206 and F-1256.", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724" } ], "site_lbl": "Tyr1173" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q68CZ2-1.1154.1154", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q68CZ2-1.1167.1167", "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": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q68CZ2-1.1206.1206", "start_pos": 1206, "end_pos": 1206, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PEAK1 Y635 phosphorylation regulates cell migration through association with Tensin3 and integrins.", "journal": "The Journal of cell biology", "date": "2022", "authors": "Zuidema A, Atherton P, Kreft M, Hoekman L, Bleijerveld OB, Nagaraj N, Chen N, Fassler R, Sonnenberg A", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "RefSeq", "id": "NP_073585", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_073585" } ], "reference": [ { "type": "PubMed", "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021" } ] }, { "title": "The Tensin-3 protein, including its SH2 domain, is phosphorylated by Src and contributes to tumorigenesis and metastasis.", "journal": "Cancer cell", "date": "2009", "authors": "Qian X, Li G, Vass WC, Papageorge A, Walker RC, Asnaghi L, Steinbach PJ, Tosato G, Hunter K, Lowy DR", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LKDKEPGSFIVRDSHSFRGA", "down_seq": "GLAMKVATPPPSVLQLNKKA", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Significantly reduced interaction with PEAK1; when associated with F-1173 and F-1256.", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724" } ], "site_lbl": "Tyr1206" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q68CZ2-1.1256.1256", "start_pos": 1256, "end_pos": 1256, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "PEAK1 Y635 phosphorylation regulates cell migration through association with Tensin3 and integrins.", "journal": "The Journal of cell biology", "date": "2022", "authors": "Zuidema A, Atherton P, Kreft M, Hoekman L, Bleijerveld OB, Nagaraj N, Chen N, Fassler R, Sonnenberg A", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "RefSeq", "id": "NP_073585", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_073585" } ], "reference": [ { "type": "PubMed", "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021" } ] }, { "title": "The Tensin-3 protein, including its SH2 domain, is phosphorylated by Src and contributes to tumorigenesis and metastasis.", "journal": "Cancer cell", "date": "2009", "authors": "Qian X, Li G, Vass WC, Papageorge A, Walker RC, Asnaghi L, Steinbach PJ, Tosato G, Hunter K, Lowy DR", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "HFLIECTPKGVRLKGCSNEP", "down_seq": "FGSLTALVCQHSITPLALPC", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "F", "comment": "Significantly reduced interaction with PEAK1; when associated with F-1173 and F-1206.", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "35687021", "url": "https://glygen.org/publication/PubMed/35687021" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "P12931-1", "kinase_gene_name": "SRC", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19732724", "url": "https://glygen.org/publication/PubMed/19732724" } ], "site_lbl": "Tyr1256" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q68CZ2-1.1255.1255", "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": 1 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 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": "Q68CZ2-1.321.321", "start_pos": 321, "end_pos": 321, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A phosphorylation switch controls the spatiotemporal activation of Rho GTPases in directional cell migration.", "journal": "Nature communications", "date": "2015", "authors": "Cao X, Kaneko T, Li JS, Liu AD, Voss C, Li SS", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "TPEKIQGSEHLYNDHGVIVD", "down_seq": "NTTDPLIRWDSYENLSADGE", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "T", "comment": "Constitutive interaction with p85 and interaction with DLC1 after EGF stimulation.", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q68CZ2-1.323.323", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q68CZ2-1.333.333", "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": "Q68CZ2-1.323.323", "start_pos": 323, "end_pos": 323, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "A phosphorylation switch controls the spatiotemporal activation of Rho GTPases in directional cell migration.", "journal": "Nature communications", "date": "2015", "authors": "Cao X, Kaneko T, Li JS, Liu AD, Voss C, Li SS", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EKIQGSEHLYNDHGVIVDYN", "down_seq": "TDPLIRWDSYENLSADGEVL", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Abolishes phosphorylation. Abolishes interaction with DLC1 and p85.", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433" } ] }, { "sequence_org": "T", "sequence_mut": "E", "comment": "Constitutive interaction with p85.", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "26166433", "url": "https://glygen.org/publication/PubMed/26166433" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Thr323" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q68CZ2-1.321.321", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q68CZ2-1.333.333", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.696.696", "start_pos": 696, "end_pos": 696, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs748272175", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748272175", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748272175", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748272175", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748272175", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748272175#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748272175", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748272175", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NGAGPELSTGPSPGSPTLDI", "down_seq": "QSIEQLNRLILELDPTFEPI", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" }, { "id": "rs748272175", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748272175" }, { "id": "rs748272175", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748272175" }, { "id": "rs748272175", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748272175#frequency_tab" }, { "id": "rs748272175", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748272175" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: num. of cancers (3); n-glyco-sequon-gain (DQS->NQS).", "chr_id": "7", "chr_pos": "47368560", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D696", "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:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.687.687", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q68CZ2-1.690.690", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q68CZ2-1.692.692", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.1021.1021", "start_pos": 1021, "end_pos": 1021, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ELSLAEPPDSLAPPSSQAFL", "down_seq": "FGTAPVGSGLPPEEDLGALL", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47303346", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1021", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": "Q68CZ2-1.1108.1108", "start_pos": 1108, "end_pos": 1108, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs745410545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745410545", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs745410545", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745410545", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs745410545", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745410545", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "QGVTLPGQPPLPEKKRASEG", "down_seq": "RSLGSVSPSSSGFSSPHSGS", "snv": [ { "evidence": [ { "id": "rs745410545", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745410545" }, { "id": "rs745410545", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs745410545" }, { "id": "rs745410545", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs745410545" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DRS->NRS).", "chr_id": "7", "chr_pos": "47303085", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1108", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q68CZ2-1.1118.1118", "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": "Q68CZ2-1.113.113", "start_pos": 113, "end_pos": 113, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SWLNSNLQHVVVIHCRGGKG", "down_seq": "IGVVISSYMHFTNVSASADQ", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "7", "chr_pos": "47428363", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R113", "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: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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q68CZ2-1.98.98", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.1140.1140", "start_pos": 1140, "end_pos": 1140, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1484225222", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1484225222", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1484225222", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1484225222", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GFSSPHSGSTISIPFPNVLP", "down_seq": "FSKASEAASPLPDSPGDKLV", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" }, { "id": "rs1484225222", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1484225222" }, { "id": "rs1484225222", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1484225222" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DFS->NFS).", "chr_id": "7", "chr_pos": "47302989", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1140", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.1129.1129", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.1149.1149", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q68CZ2-1.1154.1154", "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": "Q68CZ2-1.1167.1167", "start_pos": 1167, "end_pos": 1167, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771201580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771201580", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771201580", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771201580", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771201580", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771201580", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AASPLPDSPGDKLVIVKFVQ", "down_seq": "TSKFWYKADISREQAIAMLK", "snv": [ { "evidence": [ { "id": "rs771201580", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771201580" }, { "id": "rs771201580", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771201580" }, { "id": "rs771201580", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771201580" } ], "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": "7", "chr_pos": "47302231", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1167", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68CZ2-1.1149.1149", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q68CZ2-1.1154.1154", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q68CZ2-1.1173.1173", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.1255.1255", "start_pos": 1255, "end_pos": 1255, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1786492917", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1786492917", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1786492917", "url": "https://www.ensembl.org/id/rs1786492917", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "RHFLIECTPKGVRLKGCSNE", "down_seq": "YFGSLTALVCQHSITPLALP", "snv": [ { "evidence": [ { "id": "rs1786492917", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1786492917" }, { "id": "rs1786492917", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1786492917" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NEP->NET).", "chr_id": "7", "chr_pos": "47302953", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P1255", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q68CZ2-1.1256.1256", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.1314.1314", "start_pos": 1314, "end_pos": 1314, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1370221271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370221271", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1370221271", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370221271#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "PQTAANSAAELLKQGAACNV", "down_seq": "YLNSVEMESLTGHQAIQKAL", "snv": [ { "evidence": [ { "id": "rs1370221271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1370221271" }, { "id": "rs1370221271", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1370221271#frequency_tab" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVW->NVC).", "chr_id": "7", "chr_pos": "47283852", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1314", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": "Q68CZ2-1.1335.1335", "start_pos": 1335, "end_pos": 1335, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1471567452", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471567452", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1471567452", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471567452", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "YLNSVEMESLTGHQAIQKAL", "down_seq": "ITLVQEPPPVSTVVHFKVSA", "snv": [ { "evidence": [ { "id": "rs1471567452", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1471567452" }, { "id": "rs1471567452", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1471567452" } ], "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 (SIT->NIT).", "chr_id": "7", "chr_pos": "47283790", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1335", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q68CZ2-1.1352.1352", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.1352.1352", "start_pos": 1352, "end_pos": 1352, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1378605122", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1378605122", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1378605122", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1378605122", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "KALSITLVQEPPPVSTVVHF", "down_seq": "VSAQGITLTDNQRKLFFRRH", "snv": [ { "evidence": [ { "id": "rs1378605122", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1378605122" }, { "id": "rs1378605122", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1378605122" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KVS->NVS).", "chr_id": "7", "chr_pos": "47283738", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1352", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68CZ2-1.1335.1335", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.147.147", "start_pos": 147, "end_pos": 147, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "VSASADQALDRFAMKKFYDD", "down_seq": "VSALMQPSQKRYVQFLSGLL", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "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 (KVS->NVS).", "chr_id": "7", "chr_pos": "47424133", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "K147", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": "Q68CZ2-1.223.223", "start_pos": 223, "end_pos": 223, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2151412638", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2151412638", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2151412638", "url": "https://www.ensembl.org/id/rs2151412638", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LYQAMQPVYTSGIYNVGPEN", "down_seq": "SRICIVIEPAQLLKGDVMVK", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "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 (NPS->NLS).", "chr_id": "7", "chr_pos": "47411782", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P223", "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": "rs2151412638", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2151412638" }, { "id": "rs2151412638", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2151412638" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NRS).", "chr_id": "7", "chr_pos": "47411782", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P223", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q68CZ2-1.231.231", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q68CZ2-1.231.231", "start_pos": 231, "end_pos": 231, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "YTSGIYNVGPENPSRICIVI", "down_seq": "PAQLLKGDVMVKCYHKKYRS", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "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 (3).", "chr_id": "7", "chr_pos": "47411759", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E231", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q68CZ2-1.223.223", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q68CZ2-1.249.249", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.249.249", "start_pos": 249, "end_pos": 249, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "VIEPAQLLKGDVMVKCYHKK", "down_seq": "RSATRDVIFRLQFHTGAVQG", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "Y", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (YRS->NRS).", "chr_id": "7", "chr_pos": "47400893", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y249", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68CZ2-1.231.231", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.350.350", "start_pos": 350, "end_pos": 350, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs773729927", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773729927", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs773729927", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773729927", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs773729927", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773729927#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs773729927", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773729927", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "WDSYENLSADGEVLHTQGPV", "down_seq": "GSLYAKVRKKSSSDPGIPGG", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" }, { "id": "rs773729927", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773729927" }, { "id": "rs773729927", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs773729927" }, { "id": "rs773729927", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs773729927#frequency_tab" }, { "id": "rs773729927", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs773729927" } ], "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": "7", "chr_pos": "47369598", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D350", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68CZ2-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q68CZ2-1.333.333", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.361.361", "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": "Q68CZ2-1.361.361", "start_pos": 361, "end_pos": 361, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "rs180802444", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs180802444", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs180802444", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs180802444", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs180802444", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs180802444", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs180802444", "url": "https://www.ncbi.nlm.nih.gov/snp/rs180802444#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs180802444", "url": "http://gnomad.broadinstitute.org/awesome?query=rs180802444", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EVLHTQGPVDGSLYAKVRKK", "down_seq": "SSDPGIPGGPQAIPATNSPD", "snv": [ { "evidence": [ { "id": "rs180802444", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs180802444" }, { "id": "rs180802444", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs180802444" }, { "id": "rs180802444", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs180802444" }, { "id": "rs180802444", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs180802444#frequency_tab" }, { "id": "rs180802444", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs180802444" } ], "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": "7", "chr_pos": "47369564", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S361", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser361" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.350.350", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68CZ2-1.377.377", "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": "Q68CZ2-1.377.377", "start_pos": 377, "end_pos": 377, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs752786794", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752786794", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs752786794", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752786794", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VRKKSSSDPGIPGGPQAIPA", "down_seq": "NSPDHSDHTLSVSSDSGHST", "snv": [ { "evidence": [ { "id": "rs752786794", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs752786794" }, { "id": "rs752786794", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs752786794" } ], "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 (TNS->NNS).", "chr_id": "7", "chr_pos": "47369516", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T377", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68CZ2-1.361.361", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.386.386", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.386.386", "start_pos": 386, "end_pos": 386, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1192938898", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192938898", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1192938898", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1192938898#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1192938898", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192938898", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GIPGGPQAIPATNSPDHSDH", "down_seq": "LSVSSDSGHSTASARTDKTE", "snv": [ { "evidence": [ { "id": "rs1192938898", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1192938898" }, { "id": "rs1192938898", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1192938898#frequency_tab" }, { "id": "rs1192938898", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1192938898" } ], "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": "7", "chr_pos": "47369489", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T386", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.377.377", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.452.452", "start_pos": 452, "end_pos": 452, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs200894298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200894298", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs200894298", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200894298", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs200894298", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200894298#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs200894298", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200894298", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "FGLEDPGSSLKEMTDARSKY", "down_seq": "GTRHVVPAQVHVNGDAALKD", "snv": [ { "evidence": [ { "id": "rs200894298", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200894298" }, { "id": "rs200894298", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs200894298" }, { "id": "rs200894298", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs200894298#frequency_tab" }, { "id": "rs200894298", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs200894298" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SGT->NGT).", "chr_id": "7", "chr_pos": "47369291", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S452", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68CZ2-1.440.440", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.457.457", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.457.457", "start_pos": 457, "end_pos": 457, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "PGSSLKEMTDARSKYSGTRH", "down_seq": "VPAQVHVNGDAALKDRETDI", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "4177", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47369277", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V457", "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: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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68CZ2-1.440.440", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.452.452", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q68CZ2-1.476.476", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.476.476", "start_pos": 476, "end_pos": 476, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "HVVPAQVHVNGDAALKDRET", "down_seq": "ILDDEMPHHDLHSVDSLGTL", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "D", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "7", "chr_pos": "47369219", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D476", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q68CZ2-1.457.457", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q68CZ2-1.524.524", "start_pos": 524, "end_pos": 524, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SAHLGPFTCHKSSQNSLLSD", "down_seq": "FGSNVGEDPQGTLVPDLGLG", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47369076", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G524", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q68CZ2-1.516.516", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q68CZ2-1.530.530", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q68CZ2-1.538.538", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.530.530", "start_pos": 530, "end_pos": 530, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1469973944", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469973944", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1469973944", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469973944#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1469973944", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1469973944", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "FTCHKSSQNSLLSDGFGSNV", "down_seq": "EDPQGTLVPDLGLGMDGPYE", "snv": [ { "evidence": [ { "id": "rs1469973944", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1469973944" }, { "id": "rs1469973944", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1469973944#frequency_tab" }, { "id": "rs1469973944", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1469973944" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NVG->NVC).", "chr_id": "7", "chr_pos": "47369058", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G530", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NVG->NVS).", "chr_id": "7", "chr_pos": "47369058", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G530", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q68CZ2-1.516.516", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q68CZ2-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q68CZ2-1.538.538", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q68CZ2-1.538.538", "start_pos": 538, "end_pos": 538, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "NSLLSDGFGSNVGEDPQGTL", "down_seq": "PDLGLGMDGPYERERTFGSR", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47369034", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V538", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q68CZ2-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q68CZ2-1.530.530", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68CZ2-1.553.553", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.553.553", "start_pos": 553, "end_pos": 553, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PQGTLVPDLGLGMDGPYERE", "down_seq": "TFGSREPKQPQPLLRKPSVS", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47368988", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R553", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q68CZ2-1.538.538", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q68CZ2-1.571.571", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q68CZ2-1.573.573", "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": "Q68CZ2-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1169955340", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169955340", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1169955340", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1169955340", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MLKSKHGDNYLVLNLSEKRY", "down_seq": "LTKLNPKIMDVGWPELHAPP", "snv": [ { "evidence": [ { "id": "rs1169955340", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1169955340" }, { "id": "rs1169955340", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1169955340" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (DLT->NLT).", "chr_id": "7", "chr_pos": "47437286", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D60", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "upstream", "id": "Q68CZ2-1.78.78", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.613.613", "start_pos": 613, "end_pos": 613, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1338208831", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1338208831", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1338208831", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1338208831#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1338208831", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1338208831", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQMVVAHQYSFAPDGEARLV", "down_seq": "RCPADNPGLVQAQPRVPLTP", "snv": [ { "evidence": [ { "id": "rs1338208831", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1338208831" }, { "id": "rs1338208831", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1338208831#frequency_tab" }, { "id": "rs1338208831", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1338208831" } ], "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 (SRC->NRC).", "chr_id": "7", "chr_pos": "47368808", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "0", "site_lbl": "S613", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68CZ2-1.601.601", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q68CZ2-1.632.632", "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": "Q68CZ2-1.637.637", "start_pos": 637, "end_pos": 637, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1248816107", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248816107", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1248816107", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1248816107", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ADNPGLVQAQPRVPLTPTRG", "down_seq": "SSRVAVQRGVGSGPHPPDTQ", "snv": [ { "evidence": [ { "id": "rs1248816107", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1248816107" }, { "id": "rs1248816107", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1248816107" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (TSS->NSS).", "chr_id": "7", "chr_pos": "47368736", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T637", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q68CZ2-1.649.649", "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": "Q68CZ2-1.78.78", "start_pos": 78, "end_pos": 78, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "RYDLTKLNPKIMDVGWPELH", "down_seq": "PPLDKMCTICKAQESWLNSN", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "7", "chr_pos": "47435374", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A78", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68CZ2-1.60.60", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q68CZ2-1.98.98", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.807.807", "start_pos": 807, "end_pos": 807, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs771386207", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771386207", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs771386207", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771386207", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs771386207", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771386207#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs771386207", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771386207", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QLPFSKCAWGKAGVDYAPNL", "down_seq": "PFPSPADVKETMTPGYPQDL", "snv": [ { "evidence": [ { "id": "rs771386207", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771386207" }, { "id": "rs771386207", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs771386207" }, { "id": "rs771386207", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs771386207#frequency_tab" }, { "id": "rs771386207", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs771386207" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NLP->NLS).", "chr_id": "7", "chr_pos": "47346219", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P807", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68CZ2-1.791.791", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.802.802", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q68CZ2-1.811.811", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68CZ2-1.823.823", "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": "Q68CZ2-1.861.861", "start_pos": 861, "end_pos": 861, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MCSTPAFPVSPETPYVKTAL", "down_seq": "HPPFSPPEPPLSSPASQHKG", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47344823", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R861", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.850.850", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.866.866", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q68CZ2-1.873.873", "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": "Q68CZ2-1.911.911", "start_pos": 911, "end_pos": 911, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TLTHAVGMSESPIGPKSTML", "down_seq": "ADASSTPSFQQAFASSCTIS", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "7", "chr_pos": "47304923", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R911", "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: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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q68CZ2-1.901.901", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q68CZ2-1.914.914", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.914.914", "start_pos": 914, "end_pos": 914, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HAVGMSESPIGPKSTMLRAD", "down_seq": "SSTPSFQQAFASSCTISSNG", "snv": [ { "evidence": [ { "id": "Q68CZ2", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q68CZ2" } ], "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": "7", "chr_pos": "47304913", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A914", "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": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q68CZ2-1.901.901", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q68CZ2-1.911.911", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.941.941", "start_pos": 941, "end_pos": 941, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs757535089", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757535089", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs757535089", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757535089", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs757535089", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757535089", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QQAFASSCTISSNGPGQRRE", "down_seq": "SSSAERQWVESSPKPMVSLL", "snv": [ { "evidence": [ { "id": "rs757535089", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757535089" }, { "id": "rs757535089", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs757535089" }, { "id": "rs757535089", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs757535089" } ], "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": "7", "chr_pos": "47304832", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S941", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.952.952", "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": "Q68CZ2-1.967.967", "start_pos": 967, "end_pos": 967, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "rs1241580495", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241580495", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1241580495", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1241580495#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "RQWVESSPKPMVSLLGSGRP", "down_seq": "GSPLSAEFSGTRKDSPVLSC", "snv": [ { "evidence": [ { "id": "rs1241580495", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1241580495" }, { "id": "rs1241580495", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1241580495#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 (TGS->NGS).", "chr_id": "7", "chr_pos": "47303507", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T967", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr967" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q68CZ2-1.952.952", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q68CZ2-1.963.963", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68CZ2-1.969.969", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.978.978", "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": "Q68CZ2-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs775011054", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775011054", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs775011054", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775011054", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs775011054", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775011054#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs775011054", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775011054", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "APPLDKMCTICKAQESWLNS", "down_seq": "LQHVVVIHCRGGKGRIGVVI", "snv": [ { "evidence": [ { "id": "rs775011054", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775011054" }, { "id": "rs775011054", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs775011054" }, { "id": "rs775011054", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs775011054#frequency_tab" }, { "id": "rs775011054", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs775011054" } ], "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": "7", "chr_pos": "47435313", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N98", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q68CZ2-1.78.78", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68CZ2-1.113.113", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q68CZ2-1.1145.1145", "start_pos": 1145, "end_pos": 1145, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "HSGSTISIPFPNVLPDFSKA", "down_seq": "EAASPLPDSPGDKLVIVKFV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1145" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68CZ2-1.1129.1129", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q68CZ2-1.1149.1149", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.1154.1154", "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": "Q68CZ2-1.1149.1149", "start_pos": 1149, "end_pos": 1149, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TISIPFPNVLPDFSKASEAA", "down_seq": "PLPDSPGDKLVIVKFVQDTS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser1149" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q68CZ2-1.1129.1129", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q68CZ2-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.1154.1154", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q68CZ2-1.1167.1167", "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": 6 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.1154.1154", "start_pos": 1154, "end_pos": 1154, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "FPNVLPDFSKASEAASPLPD", "down_seq": "PGDKLVIVKFVQDTSKFWYK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ], "site_lbl": "Ser1154" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q68CZ2-1.1140.1140", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.1145.1145", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.1149.1149", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q68CZ2-1.1167.1167", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q68CZ2-1.1173.1173", "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": 5 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "IEDB", "id": "435098", "url": "https://www.iedb.org/epitope/435098" }, { "database": "IEDB", "id": "488884", "url": "https://www.iedb.org/epitope/488884" }, { "database": "IEDB", "id": "542089", "url": "https://www.iedb.org/epitope/542089" }, { "database": "IEDB", "id": "747735", "url": "https://www.iedb.org/epitope/747735" }, { "database": "IEDB", "id": "802878", "url": "https://www.iedb.org/epitope/802878" }, { "database": "IEDB", "id": "1348497", "url": "https://www.iedb.org/epitope/1348497" }, { "database": "IEDB", "id": "1351391", "url": "https://www.iedb.org/epitope/1351391" }, { "database": "IEDB", "id": "1351814", "url": "https://www.iedb.org/epitope/1351814" }, { "database": "IEDB", "id": "1358848", "url": "https://www.iedb.org/epitope/1358848" }, { "database": "IEDB", "id": "1360296", "url": "https://www.iedb.org/epitope/1360296" }, { "database": "IEDB", "id": "1366682", "url": "https://www.iedb.org/epitope/1366682" }, { "database": "IEDB", "id": "1374960", "url": "https://www.iedb.org/epitope/1374960" }, { "database": "IEDB", "id": "1376324", "url": "https://www.iedb.org/epitope/1376324" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.iedb.org/epitope/Q68CZ2", "database": "IEDB", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "MEEGHGLDLT", "down_seq": "ITERIIAVSFPAGCSEESYL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "IEDB", "id": "Q68CZ2", "url": "https://www.iedb.org/epitope/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ], "site_lbl": "Tyr11" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": "Q68CZ2-1.1293.1293", "start_pos": 1293, "end_pos": 1293, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "ALPCKLLIPERDPLEEIAES", "down_seq": "PQTAANSAAELLKQGAACNV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser1293" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": "Q68CZ2-1.1441.1441", "start_pos": 1441, "end_pos": 1441, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "IEDB", "id": "435098", "url": "https://www.iedb.org/epitope/435098" }, { "database": "IEDB", "id": "488884", "url": "https://www.iedb.org/epitope/488884" }, { "database": "IEDB", "id": "542089", "url": "https://www.iedb.org/epitope/542089" }, { "database": "IEDB", "id": "747735", "url": "https://www.iedb.org/epitope/747735" }, { "database": "IEDB", "id": "802878", "url": "https://www.iedb.org/epitope/802878" }, { "database": "IEDB", "id": "1348497", "url": "https://www.iedb.org/epitope/1348497" }, { "database": "IEDB", "id": "1351391", "url": "https://www.iedb.org/epitope/1351391" }, { "database": "IEDB", "id": "1351814", "url": "https://www.iedb.org/epitope/1351814" }, { "database": "IEDB", "id": "1358848", "url": "https://www.iedb.org/epitope/1358848" }, { "database": "IEDB", "id": "1360296", "url": "https://www.iedb.org/epitope/1360296" }, { "database": "IEDB", "id": "1366682", "url": "https://www.iedb.org/epitope/1366682" }, { "database": "IEDB", "id": "1374960", "url": "https://www.iedb.org/epitope/1374960" }, { "database": "IEDB", "id": "1376324", "url": "https://www.iedb.org/epitope/1376324" } ], "reference": [ { "type": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" } ] }, { "title": "Solving an MHC allele-specific bias in the reported immunopeptidome.", "journal": "JCI insight", "date": "2020-10-02", "authors": "Klatt Martin G, Mack Kyeara N, Bai Yang, Aretz Zita E H, Nathan Levy I, Mun Sung Soo, Dao Tao, Scheinberg David A", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "IEDB", "id": "488884", "url": "https://www.iedb.org/epitope/488884" } ], "reference": [ { "type": "PubMed", "id": "32897882", "url": "https://glygen.org/publication/PubMed/32897882" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "https://www.iedb.org/epitope/Q68CZ2", "database": "IEDB", "categories": [ "Other" ] }, { "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32897882", "url": "https://glygen.org/publication/PubMed/32897882", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HDPEQPASAIVNFVSKVMIG", "down_seq": "PKKV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "IEDB", "id": "Q68CZ2", "url": "https://www.iedb.org/epitope/Q68CZ2" }, { "database": "PubMed", "id": "32387766", "url": "https://glygen.org/publication/PubMed/32387766" }, { "database": "PubMed", "id": "32897882", "url": "https://glygen.org/publication/PubMed/32897882" } ], "site_lbl": "Ser1441" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "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": "Q68CZ2-1.332.332", "start_pos": 332, "end_pos": 332, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "YNDHGVIVDYNTTDPLIRWD", "down_seq": "YENLSADGEVLHTQGPVDGS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser332" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.321.321", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.323.323", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q68CZ2-1.333.333", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q68CZ2-1.350.350", "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": "Q68CZ2-1.333.333", "start_pos": 333, "end_pos": 333, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "NDHGVIVDYNTTDPLIRWDS", "down_seq": "ENLSADGEVLHTQGPVDGSL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Tyr333" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68CZ2-1.321.321", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q68CZ2-1.323.323", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q68CZ2-1.332.332", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CZ2-1.350.350", "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": "Q68CZ2-1.440.440", "start_pos": 440, "end_pos": 440, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QEKAELDQLLSGFGLEDPGS", "down_seq": "LKEMTDARSKYSGTRHVVPA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser440" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q68CZ2-1.452.452", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CZ2-1.457.457", "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": "Q68CZ2-1.516.516", "start_pos": 516, "end_pos": 516, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSSSEGPQSAHLGPFTCHKS", "down_seq": "QNSLLSDGFGSNVGEDPQGT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser516" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q68CZ2-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q68CZ2-1.530.530", "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": "Q68CZ2-1.571.571", "start_pos": 571, "end_pos": 571, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RERTFGSREPKQPQPLLRKP", "down_seq": "VSAQMQAYGQSSYSTQTWVR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "site_lbl": "Ser571" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q68CZ2-1.553.553", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68CZ2-1.573.573", "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": "Q68CZ2-1.601.601", "start_pos": 601, "end_pos": 601, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2009", "authors": "St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QSSYSTQTWVRQQQMVVAHQ", "down_seq": "SFAPDGEARLVSRCPADNPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ], "site_lbl": "Tyr601" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "upstream", "id": "Q68CZ2-1.613.613", "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": "Q68CZ2-1.632.632", "start_pos": 632, "end_pos": 632, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VSRCPADNPGLVQAQPRVPL", "down_seq": "PTRGTSSRVAVQRGVGSGPH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ], "site_lbl": "Thr632" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q68CZ2-1.613.613", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.637.637", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CZ2-1.649.649", "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": "Q68CZ2-1.649.649", "start_pos": 649, "end_pos": 649, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VPLTPTRGTSSRVAVQRGVG", "down_seq": "GPHPPDTQQPSPSKAFKPRF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser649" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68CZ2-1.632.632", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q68CZ2-1.637.637", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.660.660", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q68CZ2-1.662.662", "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": "Q68CZ2-1.660.660", "start_pos": 660, "end_pos": 660, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RVAVQRGVGSGPHPPDTQQP", "down_seq": "PSKAFKPRFPGDQVVNGAGP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser660" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.649.649", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68CZ2-1.662.662", "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": "Q68CZ2-1.662.662", "start_pos": 662, "end_pos": 662, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "AVQRGVGSGPHPPDTQQPSP", "down_seq": "KAFKPRFPGDQVVNGAGPEL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser662" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q68CZ2-1.649.649", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68CZ2-1.660.660", "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": "Q68CZ2-1.687.687", "start_pos": 687, "end_pos": 687, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PRFPGDQVVNGAGPELSTGP", "down_seq": "PGSPTLDIDQSIEQLNRLIL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "site_lbl": "Ser687" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "upstream", "id": "Q68CZ2-1.690.690", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.696.696", "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": "Q68CZ2-1.690.690", "start_pos": 690, "end_pos": 690, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "PGDQVVNGAGPELSTGPSPG", "down_seq": "PTLDIDQSIEQLNRLILELD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser690" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "Q68CZ2-1.687.687", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q68CZ2-1.692.692", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q68CZ2-1.696.696", "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": "Q68CZ2-1.692.692", "start_pos": 692, "end_pos": 692, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "DQVVNGAGPELSTGPSPGSP", "down_seq": "LDIDQSIEQLNRLILELDPT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ], "site_lbl": "Thr692" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.687.687", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68CZ2-1.690.690", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q68CZ2-1.696.696", "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": "Q68CZ2-1.730.730", "start_pos": 730, "end_pos": 730, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "DPTFEPIPTHMNALGSQANG", "down_seq": "VSPDSVGGGLRASSRLPDTG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser730" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q68CZ2-1.732.732", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.735.735", "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": "Q68CZ2-1.732.732", "start_pos": 732, "end_pos": 732, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "TFEPIPTHMNALGSQANGSV", "down_seq": "PDSVGGGLRASSRLPDTGEG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser732" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q68CZ2-1.730.730", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q68CZ2-1.735.735", "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": "Q68CZ2-1.735.735", "start_pos": 735, "end_pos": 735, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PIPTHMNALGSQANGSVSPD", "down_seq": "VGGGLRASSRLPDTGEGPSR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser735" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.730.730", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q68CZ2-1.732.732", "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": "Q68CZ2-1.776.776", "start_pos": 776, "end_pos": 776, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" } ] }, { "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" } ] }, { "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2009", "authors": "St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ] }, { "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "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": "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323", "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": "ATGRQGSSAEQPLGGRLRKL", "down_seq": "LGQYDNDAGGQLPFSKCAWG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "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": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" }, { "database": "PubMed", "id": "18212344", "url": "https://glygen.org/publication/PubMed/18212344" }, { "database": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" }, { "database": "PubMed", "id": "20166139", "url": "https://glygen.org/publication/PubMed/20166139" } ], "site_lbl": "Ser776" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q68CZ2-1.780.780", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68CZ2-1.791.791", "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": "Q68CZ2-1.780.780", "start_pos": 780, "end_pos": 780, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2007", "authors": "Wolf-Yadlin A, Hautaniemi S, Lauffenburger DA, White FM", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" } ] }, { "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2009", "authors": "St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395", "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": "19901323", "url": "https://glygen.org/publication/PubMed/19901323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "QGSSAEQPLGGRLRKLSLGQ", "down_seq": "DNDAGGQLPFSKCAWGKAGV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "17389395", "url": "https://glygen.org/publication/PubMed/17389395" }, { "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": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ], "site_lbl": "Tyr780" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q68CZ2-1.776.776", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.791.791", "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": "Q68CZ2-1.791.791", "start_pos": 791, "end_pos": 791, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "RLRKLSLGQYDNDAGGQLPF", "down_seq": "KCAWGKAGVDYAPNLPPFPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser791" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q68CZ2-1.776.776", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.780.780", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.802.802", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68CZ2-1.807.807", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q68CZ2-1.811.811", "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": "Q68CZ2-1.802.802", "start_pos": 802, "end_pos": 802, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Multiple myeloma phosphotyrosine proteomic profile associated with FGFR3 expression, ligand activation, and drug inhibition.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2009", "authors": "St-Germain JR, Taylor P, Tong J, Jin LL, Nikolic A, Stewart II, Ewing RM, Dharsee M, Li Z, Trudel S, Moran MF", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "NDAGGQLPFSKCAWGKAGVD", "down_seq": "APNLPPFPSPADVKETMTPG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19901323", "url": "https://glygen.org/publication/PubMed/19901323" } ], "site_lbl": "Tyr802" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.791.791", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q68CZ2-1.807.807", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.811.811", "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": "Q68CZ2-1.811.811", "start_pos": 811, "end_pos": 811, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SKCAWGKAGVDYAPNLPPFP", "down_seq": "PADVKETMTPGYPQDLDIID", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "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": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser811" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q68CZ2-1.791.791", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.802.802", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q68CZ2-1.807.807", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q68CZ2-1.823.823", "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": "Q68CZ2-1.823.823", "start_pos": 823, "end_pos": 823, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "APNLPPFPSPADVKETMTPG", "down_seq": "PQDLDIIDGRILSSKESMCS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Tyr823" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68CZ2-1.807.807", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q68CZ2-1.811.811", "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": "Q68CZ2-1.850.850", "start_pos": 850, "end_pos": 850, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "IDGRILSSKESMCSTPAFPV", "down_seq": "PETPYVKTALRHPPFSPPEP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ], "site_lbl": "Ser850" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.861.861", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q68CZ2-1.866.866", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.866.866", "start_pos": 866, "end_pos": 866, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AFPVSPETPYVKTALRHPPF", "down_seq": "PPEPPLSSPASQHKGGREPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser866" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q68CZ2-1.850.850", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q68CZ2-1.861.861", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q68CZ2-1.873.873", "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": "Q68CZ2-1.873.873", "start_pos": 873, "end_pos": 873, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "TPYVKTALRHPPFSPPEPPL", "down_seq": "SPASQHKGGREPRSCPETLT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser873" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q68CZ2-1.861.861", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q68CZ2-1.866.866", "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": 2 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q68CZ2-1.901.901", "start_pos": 901, "end_pos": 901, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "reference": [ { "type": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648", "database": "PubMed", "categories": [ "Other" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GGREPRSCPETLTHAVGMSE", "down_seq": "PIGPKSTMLRADASSTPSFQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" } ], "site_lbl": "Ser901" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q68CZ2-1.911.911", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q68CZ2-1.914.914", "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": "Q68CZ2-1.952.952", "start_pos": 952, "end_pos": 952, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "SNGPGQRRESSSSAERQWVE", "down_seq": "SPKPMVSLLGSGRPTGSPLS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser952" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.941.941", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q68CZ2-1.963.963", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68CZ2-1.967.967", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q68CZ2-1.969.969", "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": "Q68CZ2-1.963.963", "start_pos": 963, "end_pos": 963, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "SSAERQWVESSPKPMVSLLG", "down_seq": "GRPTGSPLSAEFSGTRKDSP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser963" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.952.952", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q68CZ2-1.967.967", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q68CZ2-1.969.969", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q68CZ2-1.978.978", "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": "Q68CZ2-1.969.969", "start_pos": 969, "end_pos": 969, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "WVESSPKPMVSLLGSGRPTG", "down_seq": "PLSAEFSGTRKDSPVLSCFP", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ], "site_lbl": "Ser969" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q68CZ2-1.952.952", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q68CZ2-1.963.963", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q68CZ2-1.967.967", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q68CZ2-1.978.978", "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": "Q68CZ2-1.978.978", "start_pos": 978, "end_pos": 978, "uniprot_canonical_ac": "Q68CZ2-1", "length": 1445, "uniprot_id": "TENS3_HUMAN", "protein_name": "Tensin-3", "refseq_ac": "NP_073585", "refseq_name": "tensin-3 isoform 3", "gene_name": "TNS3", "gene_names_uniprotkb": "TNS3; TEM6; TENS1; TPP", "gene_names_refseq": "TEM6; TENS1; TNS3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" } ], "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": "Q68CZ2", "url": "https://www.uniprot.org/uniprotkb/Q68CZ2" }, { "database": "iPTMnet", "id": "Q68CZ2-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2", "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": "VSLLGSGRPTGSPLSAEFSG", "down_seq": "RKDSPVLSCFPPSELQAPFH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q68CZ2", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q68CZ2" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Thr978" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "573", "end_pos": "573" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "321", "end_pos": "321" }, { "start_pos": "323", "end_pos": "323" } ] }, { "type": "snv", "site_list": [ { "start_pos": "696", "end_pos": "696" }, { "start_pos": "1021", "end_pos": "1021" }, { "start_pos": "1050", "end_pos": "1050" }, { "start_pos": "1108", "end_pos": "1108" }, { "start_pos": "1118", "end_pos": "1118" }, { "start_pos": "1129", "end_pos": "1129" }, { "start_pos": "113", "end_pos": "113" }, { "start_pos": "1140", "end_pos": "1140" }, { "start_pos": "1167", "end_pos": "1167" }, { "start_pos": "1255", "end_pos": "1255" }, { "start_pos": "1314", "end_pos": "1314" }, { "start_pos": "1335", "end_pos": "1335" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "147", "end_pos": "147" }, { "start_pos": "223", "end_pos": "223" }, { "start_pos": "231", "end_pos": "231" }, { "start_pos": "249", "end_pos": "249" }, { "start_pos": "350", "end_pos": "350" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "377", "end_pos": "377" }, { "start_pos": "386", "end_pos": "386" }, { "start_pos": "452", "end_pos": "452" }, { "start_pos": "457", "end_pos": "457" }, { "start_pos": "476", "end_pos": "476" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "530", "end_pos": "530" }, { "start_pos": "538", "end_pos": "538" }, { "start_pos": "553", "end_pos": "553" }, { "start_pos": "573", "end_pos": "573" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "613", "end_pos": "613" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "78", "end_pos": "78" }, { "start_pos": "807", "end_pos": "807" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "911", "end_pos": "911" }, { "start_pos": "914", "end_pos": "914" }, { "start_pos": "941", "end_pos": "941" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1145", "end_pos": "1145" }, { "start_pos": "1149", "end_pos": "1149" }, { "start_pos": "1154", "end_pos": "1154" }, { "start_pos": "1173", "end_pos": "1173" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "1206", "end_pos": "1206" }, { "start_pos": "1256", "end_pos": "1256" }, { "start_pos": "1293", "end_pos": "1293" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "323", "end_pos": "323" }, { "start_pos": "332", "end_pos": "332" }, { "start_pos": "333", "end_pos": "333" }, { "start_pos": "361", "end_pos": "361" }, { "start_pos": "440", "end_pos": "440" }, { "start_pos": "516", "end_pos": "516" }, { "start_pos": "571", "end_pos": "571" }, { "start_pos": "601", "end_pos": "601" }, { "start_pos": "632", "end_pos": "632" }, { "start_pos": "649", "end_pos": "649" }, { "start_pos": "660", "end_pos": "660" }, { "start_pos": "662", "end_pos": "662" }, { "start_pos": "687", "end_pos": "687" }, { "start_pos": "690", "end_pos": "690" }, { "start_pos": "692", "end_pos": "692" }, { "start_pos": "730", "end_pos": "730" }, { "start_pos": "732", "end_pos": "732" }, { "start_pos": "735", "end_pos": "735" }, { "start_pos": "776", "end_pos": "776" }, { "start_pos": "780", "end_pos": "780" }, { "start_pos": "791", "end_pos": "791" }, { "start_pos": "802", "end_pos": "802" }, { "start_pos": "811", "end_pos": "811" }, { "start_pos": "823", "end_pos": "823" }, { "start_pos": "850", "end_pos": "850" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "873", "end_pos": "873" }, { "start_pos": "901", "end_pos": "901" }, { "start_pos": "952", "end_pos": "952" }, { "start_pos": "963", "end_pos": "963" }, { "start_pos": "967", "end_pos": "967" }, { "start_pos": "969", "end_pos": "969" }, { "start_pos": "978", "end_pos": "978" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q68CZ2-1.963.963", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q68CZ2-1.967.967", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q68CZ2-1.969.969", "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": "Q9H694-1.394.394", "start_pos": 394, "end_pos": 394, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "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": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" }, { "database": "O-GlcNAc Atlas", "id": "Q9H694", "url": "https://oglcnac.org/atlas/detail/Q9H694" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" }, { "database": "O-GlcNAc Atlas", "id": "Q9H694", "url": "https://oglcnac.org/atlas/detail/Q9H694" } ], "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": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://oglcnac.org/atlas/detail/Q9H694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs747902764", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747902764", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs747902764", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747902764", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs747902764", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747902764", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1033042781", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033042781", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1033042781", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1033042781#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1033042781", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1033042781", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LMEQLDVFISIKPKPKQPSK", "down_seq": "VIVKSVERNALNMYEARKCL", "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": "Ser394", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q9H694", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q9H694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9H694" } ] } ], "snv": [ { "evidence": [ { "id": "rs747902764", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747902764" }, { "id": "rs747902764", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs747902764" }, { "id": "rs747902764", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs747902764" } ], "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": "10", "chr_pos": "58796340", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S394", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1033042781", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1033042781" }, { "id": "rs1033042781", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1033042781#frequency_tab" }, { "id": "rs1033042781", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1033042781" } ], "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": "10", "chr_pos": "58796341", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S394", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q9H694-1.402.402", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9H694-1.405.405", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H694-1.492.492", "start_pos": 492, "end_pos": 492, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "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": "rs1483409271", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483409271", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1483409271", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1483409271#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "NSLLNALNSSVSPLQSPSSG", "down_seq": "PSPTLWAPPLANTSSATGFS", "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": "Thr492", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1483409271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483409271" }, { "id": "rs1483409271", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1483409271#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": "10", "chr_pos": "58798507", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T492", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1483409271", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1483409271" }, { "id": "rs1483409271", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1483409271#frequency_tab" } ], "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": "10", "chr_pos": "58798507", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T492", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "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": "Q9H694-1.749.749", "start_pos": 749, "end_pos": 749, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "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": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" }, { "database": "O-GlcNAc Atlas", "id": "Q9H694", "url": "https://oglcnac.org/atlas/detail/Q9H694" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" }, { "database": "O-GlcNAc Atlas", "id": "Q9H694", "url": "https://oglcnac.org/atlas/detail/Q9H694" } ], "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": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] } ], "crossref": [ { "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://oglcnac.org/atlas/detail/Q9H694", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1360062333", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360062333", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1360062333", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360062333", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1488939371", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488939371", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1488939371", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1488939371#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1488939371", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1488939371", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "FDYEQKKLLATKAMLKKPVV", "down_seq": "EVRTPTNTWSGLGFSKSMPA", "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": "Thr749", "evidence": [ { "id": "35254053", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35254053" }, { "id": "Q9H694", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9H694" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "37217939", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37217939" }, { "id": "Q9H694", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q9H694" } ] } ], "snv": [ { "evidence": [ { "id": "rs1360062333", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1360062333" }, { "id": "rs1360062333", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1360062333" } ], "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": "10", "chr_pos": "58807027", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T749", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" }, { "id": "rs1488939371", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1488939371" }, { "id": "rs1488939371", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1488939371#frequency_tab" }, { "id": "rs1488939371", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1488939371" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->M).", "chr_id": "10", "chr_pos": "58807028", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T749", "disease": [ { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9H694-1.743.743", "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", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H694-1.200.200", "start_pos": 200, "end_pos": 200, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SNQVSIAGQPAGVESARVRI", "down_seq": "ELLPLVLMFELPIAGILQPV", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "10", "chr_pos": "58788421", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R200", "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: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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "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": "Q9H694-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1843106229", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1843106229", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1843106229", "url": "https://www.ensembl.org/id/rs1843106229", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VLMFELPIAGILQPVPDPNS", "down_seq": "SIQHISQTYNISVSFKQRSR", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" }, { "id": "rs1843106229", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1843106229" }, { "id": "rs1843106229", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1843106229" } ], "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 (NSP->NSS).", "chr_id": "10", "chr_pos": "58789337", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P226", "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9H694-1.232.232", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9H694-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.232.232", "start_pos": 232, "end_pos": 232, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777968525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777968525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777968525", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777968525", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PIAGILQPVPDPNSPSIQHI", "down_seq": "QTYNISVSFKQRSRMYGATV", "snv": [ { "evidence": [ { "id": "rs777968525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525" }, { "id": "rs777968525", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525" }, { "id": "rs777968525", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777968525" } ], "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 (SQT->NQT).", "chr_id": "10", "chr_pos": "58800285", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S232", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9H694-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H694-1.244.244", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.244.244", "start_pos": 244, "end_pos": 244, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NSPSIQHISQTYNISVSFKQ", "down_seq": "SRMYGATVIVRGSQNNTSAV", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "58789392", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R244", "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: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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9H694-1.226.226", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9H694-1.232.232", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.338.338", "start_pos": 338, "end_pos": 338, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2132813568", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2132813568", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2132813568", "url": "https://www.ensembl.org/id/rs2132813568", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "IHFPDPSNPQKKSTVYLQGT", "down_seq": "ESVCLARQYLMGCLPLVLMF", "snv": [ { "evidence": [ { "id": "rs2132813568", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2132813568" }, { "id": "rs2132813568", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2132813568" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IES->NES).", "chr_id": "10", "chr_pos": "58789899", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I338", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "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": "Q9H694-1.402.402", "start_pos": 402, "end_pos": 402, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ISIKPKPKQPSKSVIVKSVE", "down_seq": "NALNMYEARKCLLGLESSGV", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "R", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "10", "chr_pos": "58796365", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R402", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q9H694-1.394.394", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9H694-1.405.405", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.405.405", "start_pos": 405, "end_pos": 405, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "KPKPKQPSKSVIVKSVERNA", "down_seq": "NMYEARKCLLGLESSGVTIA", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAL->NAS).", "chr_id": "10", "chr_pos": "58796374", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L405", "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H694-1.394.394", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9H694-1.402.402", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.445.445", "start_pos": 445, "end_pos": 445, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "ATSPSPASCPAGLACPSLDI", "down_seq": "ASAGLGLTGLGLLGPTTLSL", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "58796493", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L445", "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: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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q9H694-1.462.462", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.462.462", "start_pos": 462, "end_pos": 462, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1564619979", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1564619979", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1564619979", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1564619979#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1564619979", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1564619979", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LDILASAGLGLTGLGLLGPT", "down_seq": "LSLNTSTTPNSLLNALNSSV", "snv": [ { "evidence": [ { "id": "rs1564619979", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1564619979" }, { "id": "rs1564619979", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1564619979#frequency_tab" }, { "id": "rs1564619979", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1564619979" } ], "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": "10", "chr_pos": "58798417", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T462", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9H694-1.445.445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.565.565", "start_pos": 565, "end_pos": 565, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs138338339", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138338339", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs138338339", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138338339#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs138338339", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138338339", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PPPGLTPVDVHINSMQTEGK", "down_seq": "ISAALNGHAQSPDIKYGAIS", "snv": [ { "evidence": [ { "id": "rs138338339", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs138338339" }, { "id": "rs138338339", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs138338339#frequency_tab" }, { "id": "rs138338339", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs138338339" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KIS->NIS).", "chr_id": "10", "chr_pos": "58799222", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K565", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q9H694-1.576.576", "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": "Q9H694-1.59.59", "start_pos": 59, "end_pos": 59, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ATLHSPEWSEERFRVDRKKL", "down_seq": "AMLQAAAEGKGRSGEDFFQK", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "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": "10", "chr_pos": "58513318", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E59", "keywords": [ "biomuta", "somatic", "cancer" ] }, { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "58513318", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E59", "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" } ] }, { "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q9H694-1.43.43", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "Q9H694-1.606.606", "start_pos": 606, "end_pos": 606, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs777968525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs777968525", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs777968525", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777968525", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TSSLGEKVLSANHGDPSIQT", "down_seq": "GSEQTSPKSSPTEGCNDAFV", "snv": [ { "evidence": [ { "id": "rs777968525", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525" }, { "id": "rs777968525", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs777968525" }, { "id": "rs777968525", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs777968525" } ], "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": "10", "chr_pos": "58800285", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S606", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9H694-1.612.612", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9H694-1.624.624", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.624.624", "start_pos": 624, "end_pos": 624, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1205040490", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205040490", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1205040490", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205040490", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "QTSGSEQTSPKSSPTEGCND", "down_seq": "FVEVGMPRSPSHSGNAGDLK", "snv": [ { "evidence": [ { "id": "rs1205040490", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1205040490" }, { "id": "rs1205040490", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1205040490" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NDA->NDT).", "chr_id": "10", "chr_pos": "58800901", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A624", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9H694-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9H694-1.612.612", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q9H694-1.633.633", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9H694-1.641.641", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.641.641", "start_pos": 641, "end_pos": 641, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1564621877", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1564621877", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1564621877", "url": "https://www.ensembl.org/id/rs1564621877", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "CNDAFVEVGMPRSPSHSGNA", "down_seq": "DLKQMMCPSKVSCAKRQTVE", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "589", "subjects_positive": "1", "frequency": "0.2", "sequence_org": "G", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAG->NAC).", "chr_id": "10", "chr_pos": "58800952", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G641", "disease": [ { "disease_id": "DOID:2394", "recommended_name": { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian cancer", "description": "A female reproductive organ cancer that is located_in the ovary." }, "synonyms": [ { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant Ovarian tumor", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "malignant tumour of ovary", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovarian neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "ovary neoplasm", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "primary ovarian cancer", "description": "" }, { "id": "DOID:2394", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2394", "name": "tumor of the Ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "A primary or metastatic malignant neoplasm involving the ovary. Most primary malignant ovarian neoplasms are either carcinomas (serous, mucinous, or endometrioid adenocarcinomas) or malignant germ cell tumors. Metastatic malignant neoplasms to the ovary include carcinomas, lymphomas, and melanomas." }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "cancer of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant neoplasm of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovarian tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant ovary neoplasm", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumor of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "malignant tumour of the ovary", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1564621877", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1564621877" }, { "id": "rs1564621877", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1564621877" } ], "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": "10", "chr_pos": "58800952", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "G641", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9H694-1.624.624", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q9H694-1.633.633", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9H694-1.651.651", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q9H694-1.651.651", "start_pos": 651, "end_pos": 651, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1006683706", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1006683706", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1006683706", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1006683706", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs1006683706", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1006683706#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1006683706", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1006683706", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "PRSPSHSGNAGDLKQMMCPS", "down_seq": "VSCAKRQTVELLQGTKNSHL", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" }, { "id": "rs1006683706", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1006683706" }, { "id": "rs1006683706", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1006683706" }, { "id": "rs1006683706", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1006683706#frequency_tab" }, { "id": "rs1006683706", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1006683706" } ], "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 (KVS->NVS).", "chr_id": "10", "chr_pos": "58800984", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "K651", "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q9H694-1.633.633", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9H694-1.641.641", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.672.672", "start_pos": 672, "end_pos": 672, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs375595338", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375595338", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375595338", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375595338", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375595338", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375595338#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375595338", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375595338", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "VSCAKRQTVELLQGTKNSHL", "down_seq": "STDRLLSDPELSATESPLAD", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" }, { "id": "rs375595338", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375595338" }, { "id": "rs375595338", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375595338" }, { "id": "rs375595338", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375595338#frequency_tab" }, { "id": "rs375595338", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375595338" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (HST->NST).", "chr_id": "10", "chr_pos": "58801045", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H672", "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9H694-1.679.679", "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": "Q9H694-1.743.743", "start_pos": 743, "end_pos": 743, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "YVNMQAFDYEQKKLLATKAM", "down_seq": "KKPVVTEVRTPTNTWSGLGF", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "58807009", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L743", "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: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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q9H694-1.749.749", "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": "Q9H694-1.804.804", "start_pos": 804, "end_pos": 804, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1201651719", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1201651719", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1201651719", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1201651719#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1201651719", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1201651719", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "KPTMTTTYEGSSMSLSRSNS", "down_seq": "EHLGGGSESDNWRDRNGIGP", "snv": [ { "evidence": [ { "id": "rs1201651719", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1201651719" }, { "id": "rs1201651719", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1201651719#frequency_tab" }, { "id": "rs1201651719", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1201651719" } ], "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": "10", "chr_pos": "58813863", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R804", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NSR->NSS).", "chr_id": "10", "chr_pos": "58813863", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R804", "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "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", "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": "Q9H694-1.826.826", "start_pos": 826, "end_pos": 826, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs760904194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760904194", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs760904194", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760904194", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs760904194", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760904194#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs760904194", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760904194", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLGGGSESDNWRDRNGIGPG", "down_seq": "HSEFAASIGSPKRKQNKSTE", "snv": [ { "evidence": [ { "id": "rs760904194", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760904194" }, { "id": "rs760904194", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs760904194" }, { "id": "rs760904194", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs760904194#frequency_tab" }, { "id": "rs760904194", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs760904194" } ], "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": "10", "chr_pos": "58813930", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S826", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "58813931", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S826", "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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q9H694-1.836.836", "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", "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": "Q9H694-1.855.855", "start_pos": 855, "end_pos": 855, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1424850283", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1424850283", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1424850283", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1424850283", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "GSPKRKQNKSTEHYLSSSNY", "down_seq": "DCISSLTGSNGCNLNSSFKG", "snv": [ { "evidence": [ { "id": "rs1424850283", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1424850283" }, { "id": "rs1424850283", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1424850283" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "M", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYM->NYT).", "chr_id": "10", "chr_pos": "58817592", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "M855", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9H694-1.836.836", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9H694-1.866.866", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.866.866", "start_pos": 866, "end_pos": 866, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "EHYLSSSNYMDCISSLTGSN", "down_seq": "CNLNSSFKGSDLPELFSKLG", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "10", "chr_pos": "58817625", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G866", "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": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H694-1.855.855", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.937.937", "start_pos": 937, "end_pos": 937, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "ITTFGARRKMLLAISELNKN", "down_seq": "RKLFESPNARTSFLEGGASG", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "10", "chr_pos": "58828775", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R937", "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: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": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "upstream", "id": "Q9H694-1.947.947", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9H694-1.947.947", "start_pos": 947, "end_pos": 947, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs149662454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149662454", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs149662454", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149662454", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs149662454", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149662454", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs149662454", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149662454#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs149662454", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149662454", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LLAISELNKNRRKLFESPNA", "down_seq": "TSFLEGGASGRLPRQYHSDI", "snv": [ { "evidence": [ { "id": "Q9H694", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9H694" }, { "id": "rs149662454", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149662454" }, { "id": "rs149662454", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149662454" }, { "id": "rs149662454", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149662454" }, { "id": "rs149662454", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149662454#frequency_tab" }, { "id": "rs149662454", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149662454" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAR->NAC).", "chr_id": "10", "chr_pos": "58828805", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R947", "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" ] }, { "evidence": [ { "id": "rs149662454", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149662454" }, { "id": "rs149662454", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs149662454" }, { "id": "rs149662454", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs149662454" }, { "id": "rs149662454", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs149662454#frequency_tab" }, { "id": "rs149662454", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs149662454" } ], "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": "10", "chr_pos": "58828805", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "R947", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9H694-1.937.937", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q9H694-1.26.26", "start_pos": 26, "end_pos": 26, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EPGYLAAQSDPGSNSERSTD", "down_seq": "PVPGSEDDLVAGATLHSPEW", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "site_lbl": "Ser26" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q9H694-1.31.31", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9H694-1.43.43", "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": "Q9H694-1.31.31", "start_pos": 31, "end_pos": 31, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAQSDPGSNSERSTDSPVPG", "down_seq": "EDDLVAGATLHSPEWSEERF", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "site_lbl": "Ser31" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q9H694-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H694-1.43.43", "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": "Q9H694-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "STDSPVPGSEDDLVAGATLH", "down_seq": "PEWSEERFRVDRKKLEAMLQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "site_lbl": "Ser43" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9H694-1.26.26", "categories": [ "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q9H694-1.31.31", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q9H694-1.59.59", "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": "Q9H694-1.576.576", "start_pos": 576, "end_pos": 576, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "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": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" }, { "database": "iPTMnet", "id": "Q9H694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9H694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "INSMQTEGKKISAALNGHAQ", "down_seq": "PDIKYGAISTSSLGEKVLSA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q9H694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694" } ], "site_lbl": "Ser576" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9H694-1.565.565", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9H694-1.612.612", "start_pos": 612, "end_pos": 612, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KVLSANHGDPSIQTSGSEQT", "down_seq": "PKSSPTEGCNDAFVEVGMPR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "site_lbl": "Ser612" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q9H694-1.606.606", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q9H694-1.624.624", "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": "Q9H694-1.633.633", "start_pos": 633, "end_pos": 633, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "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": "Q9H694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694-1" } ], "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": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" }, { "database": "iPTMnet", "id": "Q9H694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9H694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694", "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": "PKSSPTEGCNDAFVEVGMPR", "down_seq": "PSHSGNAGDLKQMMCPSKVS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694" }, { "database": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser633" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q9H694-1.624.624", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q9H694-1.641.641", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9H694-1.651.651", "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": "Q9H694-1.679.679", "start_pos": 679, "end_pos": 679, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TVELLQGTKNSHLHSTDRLL", "down_seq": "DPELSATESPLADKKAPGSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "site_lbl": "Ser679" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9H694-1.672.672", "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": "Q9H694-1.836.836", "start_pos": 836, "end_pos": 836, "uniprot_canonical_ac": "Q9H694-1", "length": 974, "uniprot_id": "BICC1_HUMAN", "protein_name": "Protein bicaudal C homolog 1", "refseq_ac": "NP_001073981", "refseq_name": "protein bicaudal C homolog 1", "gene_name": "BICC1", "gene_names_uniprotkb": "BICC1", "gene_names_refseq": "BICC1; BICC", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" } ], "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": "Q9H694", "url": "https://www.uniprot.org/uniprotkb/Q9H694" }, { "database": "iPTMnet", "id": "Q9H694-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q9H694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694", "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": "WRDRNGIGPGSHSEFAASIG", "down_seq": "PKRKQNKSTEHYLSSSNYMD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9H694", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9H694" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser836" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "394", "end_pos": "394" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "749", "end_pos": "749" } ] }, { "type": "snv", "site_list": [ { "start_pos": "200", "end_pos": "200" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "232", "end_pos": "232" }, { "start_pos": "244", "end_pos": "244" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "394", "end_pos": "394" }, { "start_pos": "402", "end_pos": "402" }, { "start_pos": "405", "end_pos": "405" }, { "start_pos": "445", "end_pos": "445" }, { "start_pos": "462", "end_pos": "462" }, { "start_pos": "492", "end_pos": "492" }, { "start_pos": "565", "end_pos": "565" }, { "start_pos": "59", "end_pos": "59" }, { "start_pos": "606", "end_pos": "606" }, { "start_pos": "624", "end_pos": "624" }, { "start_pos": "641", "end_pos": "641" }, { "start_pos": "651", "end_pos": "651" }, { "start_pos": "672", "end_pos": "672" }, { "start_pos": "743", "end_pos": "743" }, { "start_pos": "749", "end_pos": "749" }, { "start_pos": "804", "end_pos": "804" }, { "start_pos": "826", "end_pos": "826" }, { "start_pos": "855", "end_pos": "855" }, { "start_pos": "866", "end_pos": "866" }, { "start_pos": "937", "end_pos": "937" }, { "start_pos": "947", "end_pos": "947" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "26", "end_pos": "26" }, { "start_pos": "31", "end_pos": "31" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "576", "end_pos": "576" }, { "start_pos": "612", "end_pos": "612" }, { "start_pos": "633", "end_pos": "633" }, { "start_pos": "679", "end_pos": "679" }, { "start_pos": "836", "end_pos": "836" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q9H694-1.826.826", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9H694-1.855.855", "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": "P42771-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "P42771", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42771" } ], "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": "P42771", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42771" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42771", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42771", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "33214551", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/33214551" }, { "id": "P42771", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P42771" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": false, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 1 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycan_sites", "count": 1 }, { "field": "fuzzy_o_linked_glycans", "count": 1 } ], "sort_fields": [ "glytoucan_ac", "type", "subtype", "site_category", "site_seq", "relation", "comment" ] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 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": "P42771-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EGFLDTLVVLHRAGARLDVR", "down_seq": "AWGRLPVDLAEELGHRDVAR", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "20", "frequency": "1.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 3 filters: patient freq. (1.0%); patient count (20/1906); num. of cancers (6).", "chr_id": "9", "chr_pos": "21971037", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D108", "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" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971036", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "D108", "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: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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "9", "chr_pos": "21971037", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D108", "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: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: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: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" } ] }, { "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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.83.83", "start_pos": 83, "end_pos": 83, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LLLHGAEPNCADPATLTRPV", "down_seq": "DAAREGFLDTLVVLHRAGAR", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "12", "frequency": "0.7", "sequence_org": "H", "sequence_mut": "Y", "comment": "Somatic mutation passed 2 filters: patient count (12/1773); num. of cancers (15).", "chr_id": "9", "chr_pos": "21971112", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "H83", "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: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: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" } ] }, { "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: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: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: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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "9", "chr_pos": "21971112", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "H83", "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: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: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: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: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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971112", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "H83", "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: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" } ] }, { "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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971110", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "H83", "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: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: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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21971111", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "H83", "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" } ] }, { "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:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.84.84", "start_pos": 84, "end_pos": 84, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLHGAEPNCADPATLTRPVH", "down_seq": "AAREGFLDTLVVLHRAGARL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "12", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 2 filters: patient count (12/4799); num. of cancers (9).", "chr_id": "9", "chr_pos": "21971109", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D84", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID: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:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID: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: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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971108", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D84", "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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "9", "chr_pos": "21971108", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "D84", "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: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: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" } ] }, { "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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (9).", "chr_id": "9", "chr_pos": "21971109", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D84", "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:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID: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: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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": 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_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.101.101", "start_pos": 101, "end_pos": 101, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PVHDAAREGFLDTLVVLHRA", "down_seq": "ARLDVRDAWGRLPVDLAEEL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971058", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G101", "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: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.102.102", "start_pos": 102, "end_pos": 102, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VHDAAREGFLDTLVVLHRAG", "down_seq": "RLDVRDAWGRLPVDLAEELG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "E", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971054", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A102", "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: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" } ] }, { "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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (11).", "chr_id": "9", "chr_pos": "21971054", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A102", "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" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID: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: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: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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P42771-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "MEPAAGSSM", "down_seq": "PSADWLATAAARGRVEEVRA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21974800", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E10", "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: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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P42771-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.24.24", "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": "P42771-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "FLDTLVVLHRAGARLDVRDA", "down_seq": "GRLPVDLAEELGHRDVARYL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (11).", "chr_id": "9", "chr_pos": "21971030", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W110", "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" } ] }, { "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: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: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: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" } ] }, { "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: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": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.112.112", "start_pos": 112, "end_pos": 112, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DTLVVLHRAGARLDVRDAWG", "down_seq": "LPVDLAEELGHRDVARYLRA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "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 (4).", "chr_id": "9", "chr_pos": "21971191", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R112", "disease": [ { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "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 (5).", "chr_id": "9", "chr_pos": "21971024", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R112", "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: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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P42771-1.114.114", "start_pos": 114, "end_pos": 114, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LVVLHRAGARLDVRDAWGRL", "down_seq": "VDLAEELGHRDVARYLRAAA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "3", "frequency": "0.4", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (8).", "chr_id": "9", "chr_pos": "21971018", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P114", "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" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID: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: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: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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971019", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P114", "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:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P42771-1.116.116", "start_pos": 116, "end_pos": 116, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VLHRAGARLDVRDAWGRLPV", "down_seq": "LAEELGHRDVARYLRAAAGG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971013", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D116", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.119.119", "start_pos": 119, "end_pos": 119, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RAGARLDVRDAWGRLPVDLA", "down_seq": "ELGHRDVARYLRAAAGGTRG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "8", "frequency": "0.2", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971004", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E119", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1781", "recommended_name": { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid cancer", "description": "An endocrine gland cancer located in the thyroid gland located in the neck below the thyroid cartilage." }, "synonyms": [ { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "Thyroid gland neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "malignant tumour of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "neoplasm of thyroid gland", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid neoplasm", "description": "" }, { "id": "DOID:1781", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1781", "name": "thyroid gland cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3973", "DOID:0080524", "DOID:0080525" ], "evidence": [ { "id": "1781", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1781" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID: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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971004", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E119", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P42771-1.120.120", "start_pos": 120, "end_pos": 120, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AGARLDVRDAWGRLPVDLAE", "down_seq": "LGHRDVARYLRAAAGGTRGS", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (11).", "chr_id": "9", "chr_pos": "21971001", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E120", "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:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "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: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: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" } ] }, { "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: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" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.140.140", "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": "P42771-1.126.126", "start_pos": 126, "end_pos": 126, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VRDAWGRLPVDLAEELGHRD", "down_seq": "ARYLRAAAGGTRGSNHARID", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21970982", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V126", "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: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.140.140", "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": "P42771-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "AWGRLPVDLAEELGHRDVAR", "down_seq": "LRAAAGGTRGSNHARIDAAE", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "Y", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (8).", "chr_id": "9", "chr_pos": "21970972", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y129", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID: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: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: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" } ] }, { "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": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.140.140", "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": "P42771-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEPAAGSSMEP", "down_seq": "ADWLATAAARGRVEEVRALL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "5", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21974793", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S12", "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: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: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: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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "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 (4).", "chr_id": "9", "chr_pos": "21974793", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S12", "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: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" } ] }, { "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": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42771-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": "P42771-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "WGRLPVDLAEELGHRDVARY", "down_seq": "RAAAGGTRGSNHARIDAAEG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21970970", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L130", "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: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" } ] }, { "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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21970970", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L130", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.119.119", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.140.140", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": "P42771-1.153.153", "start_pos": 153, "end_pos": 153, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "AAGGTRGSNHARIDAAEGPS", "down_seq": "IPD", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "9", "chr_pos": "21970902", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D153", "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: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:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P42771-1.140.140", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.152.152", "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": "P42771-1.15.15", "start_pos": 15, "end_pos": 15, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "MEPAAGSSMEPSAD", "down_seq": "LATAAARGRVEEVRALLEAG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "6", "frequency": "0.2", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "9", "chr_pos": "21974784", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W15", "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: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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P42771-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.33.33", "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": "P42771-1.23.23", "start_pos": 23, "end_pos": 23, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "PAAGSSMEPSADWLATAAAR", "down_seq": "RVEEVRALLEAGALPNAPNS", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "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 (4).", "chr_id": "9", "chr_pos": "21974761", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "G23", "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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21974760", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G23", "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:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID: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": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.42.42", "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": 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": "P42771-1.24.24", "start_pos": 24, "end_pos": 24, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AAGSSMEPSADWLATAAARG", "down_seq": "VEEVRALLEAGALPNAPNSY", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974757", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "R24", "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: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: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SADWLATAAARGRVEEVRAL", "down_seq": "EAGALPNAPNSYGRRPIQVM", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974733", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L32", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "ADWLATAAARGRVEEVRALL", "down_seq": "AGALPNAPNSYGRRPIQVMM", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974731", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E33", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.53.53", "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": "P42771-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "RGRVEEVRALLEAGALPNAP", "down_seq": "SYGRRPIQVMMMGSARVAEL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974702", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N42", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.44.44", "start_pos": 44, "end_pos": 44, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "RVEEVRALLEAGALPNAPNS", "down_seq": "GRRPIQVMMMGSARVAELLL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "Y", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21974696", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "Y44", "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" } ] }, { "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.24.24", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EEVRALLEAGALPNAPNSYG", "down_seq": "RPIQVMMMGSARVAELLLLH", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974691", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "R46", "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:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.48.48", "start_pos": 48, "end_pos": 48, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VRALLEAGALPNAPNSYGRR", "down_seq": "IQVMMMGSARVAELLLLHGA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974686", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "P48", "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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (8).", "chr_id": "9", "chr_pos": "21974685", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P48", "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: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: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: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" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974685", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P48", "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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974685", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "P48", "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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": 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_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.50.50", "start_pos": 50, "end_pos": 50, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ALLEAGALPNAPNSYGRRPI", "down_seq": "VMMMGSARVAELLLLHGAEP", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21974680", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q50", "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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21974679", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "Q50", "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: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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P42771-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LLEAGALPNAPNSYGRRPIQ", "down_seq": "MMMGSARVAELLLLHGAEPN", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971207", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V51", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.32.32", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.53.53", "start_pos": 53, "end_pos": 53, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "EAGALPNAPNSYGRRPIQVM", "down_seq": "MGSARVAELLLLHGAEPNCA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "5", "frequency": "0.3", "sequence_org": "M", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971200", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "M53", "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" } ] }, { "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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.33.33", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.55.55", "start_pos": 55, "end_pos": 55, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GALPNAPNSYGRRPIQVMMM", "down_seq": "SARVAELLLLHGAEPNCADP", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971195", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G55", "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: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PNAPNSYGRRPIQVMMMGSA", "down_seq": "VAELLLLHGAEPNCADPATL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (11).", "chr_id": "9", "chr_pos": "21971187", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R58", "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: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: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: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" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.61.61", "start_pos": 61, "end_pos": 61, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PNSYGRRPIQVMMMGSARVA", "down_seq": "LLLLHGAEPNCADPATLTRP", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "9", "chr_pos": "21971178", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E61", "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: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: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" } ] }, { "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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.42.42", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.63.63", "start_pos": 63, "end_pos": 63, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "SYGRRPIQVMMMGSARVAEL", "down_seq": "LLHGAEPNCADPATLTRPVH", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971171", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L63", "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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "4", "frequency": "0.2", "sequence_org": "L", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971171", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L63", "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: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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "L", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971171", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "L63", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.44.44", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.46.46", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.68.68", "start_pos": 68, "end_pos": 68, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "PIQVMMMGSARVAELLLLHG", "down_seq": "EPNCADPATLTRPVHDAARE", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "9", "chr_pos": "21971157", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A68", "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: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:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.48.48", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.69.69", "start_pos": 69, "end_pos": 69, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "IQVMMMGSARVAELLLLHGA", "down_seq": "PNCADPATLTRPVHDAAREG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "2", "frequency": "0.3", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "9", "chr_pos": "21971154", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E69", "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: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: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" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.70.70", "start_pos": 70, "end_pos": 70, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "QVMMMGSARVAELLLLHGAE", "down_seq": "NCADPATLTRPVHDAAREGF", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "P", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "9", "chr_pos": "21971151", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P70", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.50.50", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P42771-1.51.51", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.72.72", "start_pos": 72, "end_pos": 72, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "C", "start_aa": "C", "up_seq": "MMMGSARVAELLLLHGAEPN", "down_seq": "ADPATLTRPVHDAAREGFLD", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "C", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971143", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "C72", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.53.53", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.74.74", "start_pos": 74, "end_pos": 74, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MGSARVAELLLLHGAEPNCA", "down_seq": "PATLTRPVHDAAREGFLDTL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "4", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (8).", "chr_id": "9", "chr_pos": "21971139", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D74", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID: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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21971139", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D74", "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: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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.55.55", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 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": "P42771-1.76.76", "start_pos": 76, "end_pos": 76, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SARVAELLLLHGAEPNCADP", "down_seq": "TLTRPVHDAAREGFLDTLVV", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21971133", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A76", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.58.58", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.80.80", "start_pos": 80, "end_pos": 80, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AELLLLHGAEPNCADPATLT", "down_seq": "PVHDAAREGFLDTLVVLHRA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1557", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (16).", "chr_id": "9", "chr_pos": "21971121", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R80", "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: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" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "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: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: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: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: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: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.98.98", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "ELLLLHGAEPNCADPATLTR", "down_seq": "VHDAAREGFLDTLVVLHRAG", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "2003", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "9", "chr_pos": "21971117", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P81", "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" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.61.61", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.82.82", "start_pos": 82, "end_pos": 82, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "LLLLHGAEPNCADPATLTRP", "down_seq": "HDAAREGFLDTLVVLHRAGA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "9", "chr_pos": "21971115", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V82", "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:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.63.63", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.85.85", "start_pos": 85, "end_pos": 85, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "LHGAEPNCADPATLTRPVHD", "down_seq": "AREGFLDTLVVLHRAGARLD", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971106", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A85", "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" } ] }, { "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": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "GAEPNCADPATLTRPVHDAA", "down_seq": "EGFLDTLVVLHRAGARLDVR", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971099", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "R87", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.88.88", "start_pos": 88, "end_pos": 88, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "AEPNCADPATLTRPVHDAAR", "down_seq": "GFLDTLVVLHRAGARLDVRD", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "7", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "9", "chr_pos": "21971097", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E88", "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: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:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "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" ] }, { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21971097", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E88", "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: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: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": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.68.68", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "P42771-1.69.69", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P42771-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "PNCADPATLTRPVHDAAREG", "down_seq": "LDTLVVLHRAGARLDVRDAW", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "F", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971091", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "F90", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.70.70", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.72.72", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.110.110", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.93.93", "start_pos": 93, "end_pos": 93, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ADPATLTRPVHDAAREGFLD", "down_seq": "LVVLHRAGARLDVRDAWGRL", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971081", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "T93", "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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.94.94", "start_pos": 94, "end_pos": 94, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "DPATLTRPVHDAAREGFLDT", "down_seq": "VVLHRAGARLDVRDAWGRLP", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "L", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "21971078", "ref_nt": "A", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "L94", "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: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: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": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "3", "frequency": "0.2", "sequence_org": "L", "sequence_mut": "Q", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "9", "chr_pos": "21971078", "ref_nt": "A", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "L94", "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: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": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.74.74", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P42771-1.76.76", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "P42771-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42771", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "LTRPVHDAAREGFLDTLVVL", "down_seq": "RAGARLDVRDAWGRLPVDLA", "snv": [ { "evidence": [ { "id": "P42771", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42771" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "H", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "9", "chr_pos": "21971066", "ref_nt": "T", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "H98", "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: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" } ] }, { "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": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P42771-1.80.80", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P42771-1.81.81", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "P42771-1.82.82", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P42771-1.83.83", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.84.84", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P42771-1.85.85", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.87.87", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.88.88", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P42771-1.90.90", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P42771-1.93.93", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P42771-1.94.94", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.101.101", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.102.102", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P42771-1.108.108", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.110.110", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P42771-1.112.112", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.114.114", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P42771-1.116.116", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42771-1.140.140", "start_pos": 140, "end_pos": 140, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of p16INK4A correlates with Cdk4 association.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Gump J, Stokoe D, McCormick F", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" } ] }, { "title": "The atr protein kinase controls UV-dependent upregulation of p16INK4A through inhibition of Skp2-related polyubiquitination/degradation.", "journal": "Molecular cancer research : MCR", "date": "2011", "authors": "Al-Khalaf HH, Hendrayani SF, Aboussekhra A", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "21270107", "url": "https://glygen.org/publication/PubMed/21270107" } ] }, { "title": "The interplay between p16 serine phosphorylation and arginine methylation determines its function in modulating cellular apoptosis and senescence.", "journal": "Scientific reports", "date": "2017", "authors": "Lu Y, Ma W, Li Z, Lu J, Wang X", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ] } ], "crossref": [ { "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21270107", "url": "https://glygen.org/publication/PubMed/21270107", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ELGHRDVARYLRAAAGGTRG", "down_seq": "NHARIDAAEGPSDIPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" }, { "database": "PubMed", "id": "21270107", "url": "https://glygen.org/publication/PubMed/21270107" }, { "database": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ], "site_lbl": "Ser140" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P42771-1.120.120", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P42771-1.126.126", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P42771-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P42771-1.130.130", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P42771-1.152.152", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P42771-1.153.153", "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": "P42771-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of p16INK4A correlates with Cdk4 association.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Gump J, Stokoe D, McCormick F", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" } ] }, { "title": "The atr protein kinase controls UV-dependent upregulation of p16INK4A through inhibition of Skp2-related polyubiquitination/degradation.", "journal": "Molecular cancer research : MCR", "date": "2011", "authors": "Al-Khalaf HH, Hendrayani SF, Aboussekhra A", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "21270107", "url": "https://glygen.org/publication/PubMed/21270107" } ] }, { "title": "The interplay between p16 serine phosphorylation and arginine methylation determines its function in modulating cellular apoptosis and senescence.", "journal": "Scientific reports", "date": "2017", "authors": "Lu Y, Ma W, Li Z, Lu J, Wang X", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ] } ], "crossref": [ { "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "21270107", "url": "https://glygen.org/publication/PubMed/21270107", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AAAGGTRGSNHARIDAAEGP", "down_seq": "DIPD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" }, { "database": "PubMed", "id": "21270107", "url": "https://glygen.org/publication/PubMed/21270107" }, { "database": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ], "site_lbl": "Ser152" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "P42771-1.140.140", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.153.153", "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": "P42771-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of p16INK4A correlates with Cdk4 association.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Gump J, Stokoe D, McCormick F", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" } ] }, { "title": "The interplay between p16 serine phosphorylation and arginine methylation determines its function in modulating cellular apoptosis and senescence.", "journal": "Scientific reports", "date": "2017", "authors": "Lu Y, Ma W, Li Z, Lu J, Wang X", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ] } ], "crossref": [ { "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEPAAG", "down_seq": "SMEPSADWLATAAARGRVEE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" }, { "database": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ], "site_lbl": "Ser7" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P42771-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P42771-1.8.8", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P42771-1.24.24", "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": "P42771-1.8.8", "start_pos": 8, "end_pos": 8, "uniprot_canonical_ac": "P42771-1", "length": 156, "uniprot_id": "CDN2A_HUMAN", "protein_name": "Cyclin-dependent kinase inhibitor 2A", "refseq_ac": "NP_000068", "refseq_name": "cyclin-dependent kinase inhibitor 2A isoform p16INK4a", "gene_name": "CDKN2A", "gene_names_uniprotkb": "CDKN2A; CDKN2; MLM; MTS1", "gene_names_refseq": "ARF; CAI2; CDK4I; CDKN2A; CDKN2; CMM2; INK4A; INK4; MLM; MTS-1; MTS1; P14ARF; P14; P16-INK4A; P16INK4A; P16INK4; P16; P19ARF; P19; TP16", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "IKKbeta specifically binds to P16 and phosphorylates Ser8 of P16.", "journal": "Biochemical and biophysical research communications", "date": "2010", "authors": "Guo Y, Yuan C, Weghorst CM, Li J", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "20152798", "url": "https://glygen.org/publication/PubMed/20152798" } ] }, { "title": "Phosphorylation of p16INK4A correlates with Cdk4 association.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "Gump J, Stokoe D, McCormick F", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" } ] }, { "title": "The interplay between p16 serine phosphorylation and arginine methylation determines its function in modulating cellular apoptosis and senescence.", "journal": "Scientific reports", "date": "2017", "authors": "Lu Y, Ma W, Li Z, Lu J, Wang X", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" } ], "reference": [ { "type": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ] } ], "crossref": [ { "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20152798", "url": "https://glygen.org/publication/PubMed/20152798", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MEPAAGS", "down_seq": "MEPSADWLATAAARGRVEEV", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O14920-1", "kinase_gene_name": "IKBKB", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" }, { "database": "PubMed", "id": "20152798", "url": "https://glygen.org/publication/PubMed/20152798" } ], "site_lbl": "Ser8" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P42771", "url": "https://www.uniprot.org/uniprotkb/P42771" }, { "database": "PubMed", "id": "12529334", "url": "https://glygen.org/publication/PubMed/12529334" }, { "database": "iPTMnet", "id": "P42771", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P42771" }, { "database": "PubMed", "id": "28120917", "url": "https://glygen.org/publication/PubMed/28120917" } ], "site_lbl": "Ser8" } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "83", "end_pos": "83" }, { "start_pos": "84", "end_pos": "84" }, { "start_pos": "101", "end_pos": "101" }, { "start_pos": "102", "end_pos": "102" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "110", "end_pos": "110" }, { "start_pos": "112", "end_pos": "112" }, { "start_pos": "114", "end_pos": "114" }, { "start_pos": "116", "end_pos": "116" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "120", "end_pos": "120" }, { "start_pos": "126", "end_pos": "126" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "153", "end_pos": "153" }, { "start_pos": "15", "end_pos": "15" }, { "start_pos": "23", "end_pos": "23" }, { "start_pos": "24", "end_pos": "24" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "44", "end_pos": "44" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "48", "end_pos": "48" }, { "start_pos": "50", "end_pos": "50" }, { "start_pos": "51", "end_pos": "51" }, { "start_pos": "53", "end_pos": "53" }, { "start_pos": "55", "end_pos": "55" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "61", "end_pos": "61" }, { "start_pos": "63", "end_pos": "63" }, { "start_pos": "68", "end_pos": "68" }, { "start_pos": "69", "end_pos": "69" }, { "start_pos": "70", "end_pos": "70" }, { "start_pos": "72", "end_pos": "72" }, { "start_pos": "74", "end_pos": "74" }, { "start_pos": "76", "end_pos": "76" }, { "start_pos": "80", "end_pos": "80" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "82", "end_pos": "82" }, { "start_pos": "85", "end_pos": "85" }, { "start_pos": "87", "end_pos": "87" }, { "start_pos": "88", "end_pos": "88" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "93", "end_pos": "93" }, { "start_pos": "94", "end_pos": "94" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "140", "end_pos": "140" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "8", "end_pos": "8" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P42771-1.0.0", "categories": [ "glycosylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P42771-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P42771-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P42771-1.12.12", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P42771-1.15.15", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P42771-1.23.23", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P42771-1.24.24", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P84243-1.11.11", "start_pos": 11, "end_pos": 11, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Modification of histones by sugar beta-N-acetylglucosamine (GlcNAc) occurs on multiple residues, including histone H3 serine 10, and is cell cycle-regulated.", "journal": "The Journal of biological chemistry", "date": "2011", "authors": "Zhang S, Roche K, Nasheuer HP, Lowndes NF", "evidence": [ { "database": "O-GlcNAc Database", "id": "P84243", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243" } ], "reference": [ { "type": "PubMed", "id": "21896475", "url": "https://glygen.org/publication/PubMed/21896475" } ] }, { "title": "GlcNAcylation of histone H2B facilitates its monoubiquitination.", "journal": "Nature", "date": "2011", "authors": "Fujiki R, Hashiba W, Sekine H, Yokoyama A, Chikanishi T, Ito S, Imai Y, Kim J, He HH, Igarashi K, Kanno J, Ohtake F, Kitagawa H, Roeder RG, Brown M, Kato S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P84243", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243" } ], "reference": [ { "type": "PubMed", "id": "22121020", "url": "https://glygen.org/publication/PubMed/22121020" } ] }, { "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": "P84243", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243" } ], "reference": [ { "type": "PubMed", "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447" } ] }, { "title": "Methylation-directed glycosylation of chromatin factors represses retrotransposon promoters.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2020", "authors": "Boulard M, Rucli S, Edwards JR, Bestor TH", "evidence": [ { "database": "O-GlcNAc Database", "id": "P84243", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243" } ], "reference": [ { "type": "PubMed", "id": "32522876", "url": "https://glygen.org/publication/PubMed/32522876" } ] }, { "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": "P84243", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243" } ], "reference": [ { "type": "PubMed", "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054" } ] }, { "title": "Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Goto H, Tomono Y, Ajiro K, Kosako H, Fujita M, Sakurai M, Okawa K, Iwamatsu A, Okigaki T, Takahashi T, Inagaki M", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" } ] }, { "title": "Chromatin remodeling and neuronal response: multiple signaling pathways induce specific histone H3 modifications and early gene expression in hippocampal neurons.", "journal": "Journal of cell science", "date": "2003", "authors": "Crosio C, Heitz E, Allis CD, Borrelli E, Sassone-Corsi P", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "14625384", "url": "https://glygen.org/publication/PubMed/14625384" } ] }, { "title": "Phosphorylation of histone H3 at serine 10 is indispensable for neoplastic cell transformation.", "journal": "Cancer research", "date": "2005", "authors": "Choi HS, Choi BY, Cho YY, Mizuno H, Kang BS, Bode AM, Dong Z", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15994958", "url": "https://glygen.org/publication/PubMed/15994958" } ] }, { "title": "MSK activation and physiological roles.", "journal": "Frontiers in bioscience : a journal and virtual library", "date": "2008", "authors": "Arthur JS", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "18508628", "url": "https://glygen.org/publication/PubMed/18508628" } ] }, { "title": "Regulation of ultraviolet B-induced phosphorylation of histone H3 at serine 10 by Fyn kinase.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "He Z, Cho YY, Ma WY, Choi HS, Bode AM, Dong Z", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15537652", "url": "https://glygen.org/publication/PubMed/15537652" } ] }, { "title": "Arsenite-induced phosphorylation of histone H3 at serine 10 is mediated by Akt1, extracellular signal-regulated kinase 2, and p90 ribosomal S6 kinase 2 but not mitogen- and stress-activated protein kinase 1.", "journal": "The Journal of biological chemistry", "date": "2003", "authors": "He Z, Ma WY, Liu G, Zhang Y, Bode AM, Dong Z", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "12529330", "url": "https://glygen.org/publication/PubMed/12529330" } ] }, { "title": "Cascade of distinct histone modifications during collagenase gene activation.", "journal": "Molecular and cellular biology", "date": "2003", "authors": "Martens JH, Verlaan M, Kalkhoven E, Zantema A", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "12588998", "url": "https://glygen.org/publication/PubMed/12588998" } ] }, { "title": "Loss of p53 has site-specific effects on histone H3 modification, including serine 10 phosphorylation important for maintenance of ploidy.", "journal": "Cancer research", "date": "2003", "authors": "Allison SJ, Milner J", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "14583461", "url": "https://glygen.org/publication/PubMed/14583461" } ] }, { "title": "Phosphorylation of serine 10 in histone H3 is functionally linked in vitro and in vivo to Gcn5-mediated acetylation at lysine 14.", "journal": "Molecular cell", "date": "2000", "authors": "Lo WS, Trievel RC, Rojas JR, Duggan L, Hsu JY, Allis CD, Marmorstein R, Berger SL", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "10911986", "url": "https://glygen.org/publication/PubMed/10911986" } ] }, { "title": "Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails.", "journal": "Genes & development", "date": "2001", "authors": "Zhang Y, Reinberg D", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "11562345", "url": "https://glygen.org/publication/PubMed/11562345" } ] }, { "title": "MSK2 and MSK1 mediate the mitogen- and stress-induced phosphorylation of histone H3 and HMG-14.", "journal": "The EMBO journal", "date": "2003", "authors": "Soloaga A, Thomson S, Wiggin GR, Rampersaud N, Dyson MH, Hazzalin CA, Mahadevan LC, Arthur JS", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "12773393", "url": "https://glygen.org/publication/PubMed/12773393" } ] }, { "title": "Requirement of Rsk-2 for epidermal growth factor-activated phosphorylation of histone H3.", "journal": "Science (New York, N.Y.)", "date": "1999", "authors": "Sassone-Corsi P, Mizzen CA, Cheung P, Crosio C, Monaco L, Jacquot S, Hanauer A, Allis CD", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "10436156", "url": "https://glygen.org/publication/PubMed/10436156" } ] }, { "title": "Ectopic localization of phosphorylated histone H3 in Alzheimer's disease: a mitotic catastrophe?", "journal": "Acta neuropathologica", "date": "2003", "authors": "Ogawa O, Zhu X, Lee HG, Raina A, Obrenovich ME, Bowser R, Ghanbari HA, Castellani RJ, Perry G, Smith MA", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "12677454", "url": "https://glygen.org/publication/PubMed/12677454" } ] }, { "title": "Chromatin modification of the trefoil factor 1 gene in human breast cancer cells by the Ras/mitogen-activated protein kinase pathway.", "journal": "Cancer research", "date": "2006", "authors": "Espino PS, Li L, He S, Yu J, Davie JR", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "16651411", "url": "https://glygen.org/publication/PubMed/16651411" } ] }, { "title": "Basal c-Jun N-terminal kinases promote mitotic progression through histone H3 phosphorylation.", "journal": "Cell cycle (Georgetown, Tex.)", "date": "2008", "authors": "Lee K, Song K", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "18256527", "url": "https://glygen.org/publication/PubMed/18256527" } ] }, { "title": "Aurora-B phosphorylates Histone H3 at serine28 with regard to the mitotic chromosome condensation.", "journal": "Genes to cells : devoted to molecular & cellular mechanisms", "date": "2002", "authors": "Goto H, Yasui Y, Nigg EA, Inagaki M", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "11856369", "url": "https://glygen.org/publication/PubMed/11856369" } ] }, { "title": "Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase.", "journal": "Nucleic acids research", "date": "2003", "authors": "Preuss U, Landsberg G, Scheidtmann KH", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "12560483", "url": "https://glygen.org/publication/PubMed/12560483" } ] }, { "title": "The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment.", "journal": "Genes & development", "date": "2005", "authors": "Dai J, Sultan S, Taylor SS, Higgins JM", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610" } ] }, { "title": "Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2005", "authors": "Hake SB, Garcia BA, Kauer M, Baker SP, Shabanowitz J, Hunt DF, Allis CD", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689" } ] }, { "title": "Modifications of human histone H3 variants during mitosis.", "journal": "Biochemistry", "date": "2005", "authors": "Garcia BA, Barber CM, Hake SB, Ptak C, Turner FB, Busby SA, Shabanowitz J, Moran RG, Allis CD, Hunt DF", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ] } ], "crossref": [ { "id": "21896475", "url": "https://glygen.org/publication/PubMed/21896475", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "22121020", "url": "https://glygen.org/publication/PubMed/22121020", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28510447", "url": "https://glygen.org/publication/PubMed/28510447", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32522876", "url": "https://glygen.org/publication/PubMed/32522876", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34229054", "url": "https://glygen.org/publication/PubMed/34229054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2102735500", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735500", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102735500", "url": "https://www.ensembl.org/id/rs2102735500", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2102735498", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735498", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102735498", "url": "https://www.ensembl.org/id/rs2102735498", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2143631409", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143631409", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2143631409", "url": "https://www.ensembl.org/id/rs2143631409", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14625384", "url": "https://glygen.org/publication/PubMed/14625384", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15994958", "url": "https://glygen.org/publication/PubMed/15994958", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18508628", "url": "https://glygen.org/publication/PubMed/18508628", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15537652", "url": "https://glygen.org/publication/PubMed/15537652", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12529330", "url": "https://glygen.org/publication/PubMed/12529330", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12588998", "url": "https://glygen.org/publication/PubMed/12588998", "database": "PubMed", "categories": [ "Other" ] }, { "id": "14583461", "url": "https://glygen.org/publication/PubMed/14583461", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "10911986", "url": "https://glygen.org/publication/PubMed/10911986", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11562345", "url": "https://glygen.org/publication/PubMed/11562345", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12773393", "url": "https://glygen.org/publication/PubMed/12773393", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "10436156", "url": "https://glygen.org/publication/PubMed/10436156", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12677454", "url": "https://glygen.org/publication/PubMed/12677454", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16651411", "url": "https://glygen.org/publication/PubMed/16651411", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18256527", "url": "https://glygen.org/publication/PubMed/18256527", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11856369", "url": "https://glygen.org/publication/PubMed/11856369", "database": "PubMed", "categories": [ "Other" ] }, { "id": "12560483", "url": "https://glygen.org/publication/PubMed/12560483", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "MARTKQTARK", "down_seq": "TGGKAPRKQLATKAARKSAP", "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": "Ser11", "evidence": [ { "id": "21896475", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/21896475" }, { "id": "P84243", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P84243" }, { "id": "22121020", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22121020" }, { "id": "28510447", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/28510447" }, { "id": "32522876", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32522876" }, { "id": "34229054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34229054" } ] } ], "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "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": "75779143", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S11", "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": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" }, { "id": "rs2102735500", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735500" }, { "id": "rs2102735500", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102735500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "1", "chr_pos": "226064383", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S11", "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": "rs2102735498", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735498" }, { "id": "rs2102735498", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102735498" }, { "id": "rs2143631409", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2143631409" }, { "id": "rs2143631409", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2143631409" } ], "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": "226064382", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S11", "keywords": [ "ebi", "germline", "disease" ], "disease": [ { "disease_id": "DOID:0051012", "recommended_name": { "id": "DOID:0051012", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0051012", "name": "Bryant-Li-Bhoj neurodevelopmental syndrome 2", "description": "A Bryant-Li-Bhoj neurodevelopmental syndrome that is characterized predominantly by moderate to severe global developmental delay with impaired intellectual development, poor or absent speech, and delayed motor milestones nd that has_material_basis_in heterozygous mutation in the H3F3B gene on chromosome 17q25." }, "synonyms": [ { "id": "MONDO:0030607", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0030607", "name": "Bryant-Li-Bhoj neurodevelopmental syndrome 2", "description": "" }, { "id": "MONDO:0030607", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0030607", "name": "BRYLIB2", "description": "" }, { "id": "MIM:619721", "resource": "MIM", "url": "https://www.omim.org/entry/619721", "name": "Bryant-Li-Bhoj neurodevelopmental syndrome 2", "description": "Bryant-Li-Bhoj neurodevelopmental syndrome 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "619721", "database": "MIM", "url": "https://www.omim.org/entry/619721" }, { "id": "0051012", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0051012" } ] } ] }, { "evidence": [ { "id": "rs2102735500", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735500" }, { "id": "rs2102735500", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102735500" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "W", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->W).", "chr_id": "1", "chr_pos": "226064383", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S11", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O75582-1", "kinase_gene_name": "RPS6KA5", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" }, { "database": "PubMed", "id": "14625384", "url": "https://glygen.org/publication/PubMed/14625384" }, { "database": "PubMed", "id": "15994958", "url": "https://glygen.org/publication/PubMed/15994958" }, { "database": "PubMed", "id": "18508628", "url": "https://glygen.org/publication/PubMed/18508628" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "P06241-1", "kinase_gene_name": "FYN", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "15537652", "url": "https://glygen.org/publication/PubMed/15537652" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "P17612-1", "kinase_gene_name": "PRKACA", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "P31749-1", "kinase_gene_name": "AKT1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "12529330", "url": "https://glygen.org/publication/PubMed/12529330" }, { "database": "PubMed", "id": "12588998", "url": "https://glygen.org/publication/PubMed/12588998" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "P51812-1", "kinase_gene_name": "RPS6KA3", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" }, { "database": "PubMed", "id": "14625384", "url": "https://glygen.org/publication/PubMed/14625384" }, { "database": "PubMed", "id": "15994958", "url": "https://glygen.org/publication/PubMed/15994958" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "Q15418-1", "kinase_gene_name": "RPS6KA1", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" }, { "database": "PubMed", "id": "14625384", "url": "https://glygen.org/publication/PubMed/14625384" }, { "database": "PubMed", "id": "15994958", "url": "https://glygen.org/publication/PubMed/15994958" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "Q96GD4-1", "kinase_gene_name": "AURKB", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" }, { "database": "PubMed", "id": "12588998", "url": "https://glygen.org/publication/PubMed/12588998" }, { "database": "PubMed", "id": "14583461", "url": "https://glygen.org/publication/PubMed/14583461" } ], "site_lbl": "Ser11" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; alternate; by AURKB, AURKC, RPS6KA3, RPS6KA4 and RPS6KA5", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10911986", "url": "https://glygen.org/publication/PubMed/10911986" }, { "database": "PubMed", "id": "11562345", "url": "https://glygen.org/publication/PubMed/11562345" }, { "database": "PubMed", "id": "12529330", "url": "https://glygen.org/publication/PubMed/12529330" }, { "database": "PubMed", "id": "12773393", "url": "https://glygen.org/publication/PubMed/12773393" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "PubMed", "id": "10436156", "url": "https://glygen.org/publication/PubMed/10436156" }, { "database": "PubMed", "id": "12677454", "url": "https://glygen.org/publication/PubMed/12677454" }, { "database": "PubMed", "id": "14583461", "url": "https://glygen.org/publication/PubMed/14583461" }, { "database": "PubMed", "id": "16651411", "url": "https://glygen.org/publication/PubMed/16651411" }, { "database": "PubMed", "id": "18256527", "url": "https://glygen.org/publication/PubMed/18256527" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" }, { "database": "PubMed", "id": "11856369", "url": "https://glygen.org/publication/PubMed/11856369" }, { "database": "PubMed", "id": "12560483", "url": "https://glygen.org/publication/PubMed/12560483" }, { "database": "PubMed", "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610" }, { "database": "PubMed", "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689" }, { "database": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ], "site_lbl": "Ser11" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P84243-1.29.29", "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": 8 } ], "sort_fields": [ "kinase_uniprot_canonical_ac", "kinase_gene_name", "residue", "comment", "site_lbl" ] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 4 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 3 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 25 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P84243-1.33.33", "start_pos": 33, "end_pos": 33, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "beta-N-Acetylglucosamine (O-GlcNAc) is a novel regulator of mitosis-specific phosphorylations on histone H3.", "journal": "The Journal of biological chemistry", "date": "2012", "authors": "Fong JJ, Nguyen BL, Bridger R, Medrano EE, Wells L, Pan S, Sifers RN", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "P84243", "url": "https://oglcnac.org/atlas/detail/P84243" } ], "reference": [ { "type": "PubMed", "id": "22371497", "url": "https://glygen.org/publication/PubMed/22371497" } ] } ], "crossref": [ { "id": "22371497", "url": "https://glygen.org/publication/PubMed/22371497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://oglcnac.org/atlas/detail/P84243", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2545911125", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2545911125", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2545911125", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2545911125", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GGKAPRKQLATKAARKSAPS", "down_seq": "GGVKKPHRYRPGTVALREIR", "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": "Thr33", "evidence": [ { "id": "22371497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/22371497" }, { "id": "P84243", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/P84243" } ] } ], "snv": [ { "evidence": [ { "id": "rs2545911125", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2545911125" }, { "id": "rs2545911125", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2545911125" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->I).", "chr_id": "17", "chr_pos": "226064449", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T33", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P84243-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P84243-1.46.46", "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": "P84243-1.106.107", "start_pos": 106, "end_pos": 107, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "DNAJC9 integrates heat shock molecular chaperones into the histone chaperone network.", "journal": "Molecular cell", "date": "2021", "authors": "Hammond CM, Bao H, Hendriks IA, Carraro M, Garcia-Nieto A, Liu Y, Reveron-Gomez N, Spanos C, Chen L, Rappsilber J, Nielsen ML, Patel DJ, Huang H, Groth A", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "reference": [ { "type": "PubMed", "id": "33857403", "url": "https://glygen.org/publication/PubMed/33857403" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "33857403", "url": "https://glygen.org/publication/PubMed/33857403", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "ED", "start_aa": "E", "up_seq": "QSAAIGALQEASEAYLVGLF", "down_seq": "TNLCAIHAKRVTIMPKDIQL", "mutagenesis": [ { "sequence_org": "ED", "sequence_mut": "AA", "comment": "Loss of interaction with DNAJC9, but not with other histone chaperones, such as ASF1A, MCCM2, NASP or SPT2.", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "33857403", "url": "https://glygen.org/publication/PubMed/33857403" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P84243-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P84243-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P84243-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": false, "mutagenesis_flag": true, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P84243-1.43.43", "start_pos": 43, "end_pos": 43, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure and function of human histone H3.Y nucleosome.", "journal": "Nucleic acids research", "date": "2016", "authors": "Kujirai T, Horikoshi N, Sato K, Maehara K, Machida S, Osakabe A, Kimura H, Ohkawa Y, Kurumizaka H", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "reference": [ { "type": "PubMed", "id": "27016736", "url": "https://glygen.org/publication/PubMed/27016736" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "27016736", "url": "https://glygen.org/publication/PubMed/27016736", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TKAARKSAPSTGGVKKPHRY", "down_seq": "PGTVALREIRRYQKSTELLI", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "K", "comment": "Reduced binding of histone H1 to histone H3.3-containing nucleosomes.", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "27016736", "url": "https://glygen.org/publication/PubMed/27016736" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P84243-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P84243-1.33.33", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P84243-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.46.46", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P84243-1.58.58", "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": "P84243-1.6.6", "start_pos": 6, "end_pos": 6, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Histone serotonylation is a permissive modification that enhances TFIID binding to H3K4me3.", "journal": "Nature", "date": "2019", "authors": "Farrelly LA, Thompson RE, Zhao S, Lepack AE, Lyu Y, Bhanu NV, Zhang B, Loh YE, Ramakrishnan A, Vadodaria KC, Heard KJ, Erikson G, Nakadai T, Bastle RM, Lukasak BJ, Zebroski H 3rd, Alenina N, Bader M, Berton O, Roeder RG, Molina H, Gage FH, Shen L, Garcia BA, Li H, Muir TW, Maze I", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "reference": [ { "type": "PubMed", "id": "30867594", "url": "https://glygen.org/publication/PubMed/30867594" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "30867594", "url": "https://glygen.org/publication/PubMed/30867594", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "MARTK", "down_seq": "TARKSTGGKAPRKQLATKAA", "mutagenesis": [ { "sequence_org": "Q", "sequence_mut": "A", "comment": "Abolished serotonylation by TGM2.", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "30867594", "url": "https://glygen.org/publication/PubMed/30867594" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 3, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P84243-1.12.12", "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": "P84243-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KAPRKQLATKAARKSAPSTG", "down_seq": "VKKPHRYRPGTVALREIRRY", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "R", "comment": "Somatic mutation passed 2 filters: patient freq. (1.1%); num. of cancers (3).", "chr_id": "1", "chr_pos": "226064454", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "G35", "keywords": [ "biomuta", "somatic", "cancer", "disease" ], "disease": [ { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID: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" } ] } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P84243-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P84243-1.33.33", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P84243-1.46.46", "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": "P84243-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QSAAIGALQEASEAYLVGLF", "down_seq": "DTNLCAIHAKRVTIMPKDIQ", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "75778690", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E106", "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: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": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P84243-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P84243-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.106.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P84243-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P84243-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P84243-1.10.10", "start_pos": 10, "end_pos": 10, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2102735490", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735490", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102735490", "url": "https://www.ensembl.org/id/rs2102735490", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MARTKQTAR", "down_seq": "STGGKAPRKQLATKAARKSA", "snv": [ { "evidence": [ { "id": "rs2102735490", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735490" }, { "id": "rs2102735490", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102735490" } ], "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": "226064381", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K10", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P84243-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P84243-1.29.29", "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": "P84243-1.115.115", "start_pos": 115, "end_pos": 115, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EASEAYLVGLFEDTNLCAIH", "down_seq": "KRVTIMPKDIQLARRIRGER", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "75778662", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "A115", "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: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": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P84243-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P84243-1.106.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P84243-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P84243-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "upstream", "id": "P84243-1.130.130", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P84243-1.130.130", "start_pos": 130, "end_pos": 130, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LCAIHAKRVTIMPKDIQLAR", "down_seq": "IRGERA", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "1", "chr_pos": "226071457", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R130", "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: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": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "P84243-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P84243-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "MA", "down_seq": "TKQTARKSTGGKAPRKQLAT", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "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": "1", "chr_pos": "226064358", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R3", "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: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: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": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "G", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "1", "chr_pos": "226064358", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "R3", "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: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: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": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P84243-1.12.12", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": "P84243-1.5.5", "start_pos": 5, "end_pos": 5, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2102735447", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735447", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2102735447", "url": "https://www.ensembl.org/id/rs2102735447", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MART", "down_seq": "QTARKSTGGKAPRKQLATKA", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "K", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "17", "chr_pos": "75779161", "ref_nt": "T", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K5", "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:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "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" ] }, { "evidence": [ { "id": "rs2102735447", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2102735447" }, { "id": "rs2102735447", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2102735447" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KQT->NQT).", "chr_id": "1", "chr_pos": "226064366", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K5", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P84243-1.12.12", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "P84243-1.64.64", "start_pos": 64, "end_pos": 64, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PGTVALREIRRYQKSTELLI", "down_seq": "KLPFQRLVREIAQDFKTDLR", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "55594", "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": "226065717", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R64", "disease": [ { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID: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": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "P84243-1.46.46", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P84243-1.58.58", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P84243-1.81.81", "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": "P84243-1.67.67", "start_pos": 67, "end_pos": 67, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VALREIRRYQKSTELLIRKL", "down_seq": "FQRLVREIAQDFKTDLRFQS", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "75778893", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P67", "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: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": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P84243-1.58.58", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P84243-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P84243-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P84243-1.87.87", "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": "P84243-1.98.98", "start_pos": 98, "end_pos": 98, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DFKTDLRFQSAAIGALQEAS", "down_seq": "AYLVGLFEDTNLCAIHAKRV", "snv": [ { "evidence": [ { "id": "P84243", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P84243" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "17", "chr_pos": "75778714", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E98", "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: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: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": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P84243-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P84243-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P84243-1.106.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P84243-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P84243-1.108.108", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P84243-1.115.115", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P84243-1.108.108", "start_pos": 108, "end_pos": 108, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AAIGALQEASEAYLVGLFED", "down_seq": "NLCAIHAKRVTIMPKDIQLA", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "site_lbl": "Thr108" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "P84243-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.106.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P84243-1.106.106", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P84243-1.115.115", "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": "P84243-1.12.12", "start_pos": 12, "end_pos": 12, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Chk1 is a histone H3 threonine 11 kinase that regulates DNA damage-induced transcriptional repression.", "journal": "Cell", "date": "2008", "authors": "Shimada M, Niida H, Zineldeen DH, Tagami H, Tanaka M, Saito H, Nakanishi M", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "18243098", "url": "https://glygen.org/publication/PubMed/18243098" } ] }, { "title": "Novel mitosis-specific phosphorylation of histone H3 at Thr11 mediated by Dlk/ZIP kinase.", "journal": "Nucleic acids research", "date": "2003", "authors": "Preuss U, Landsberg G, Scheidtmann KH", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "12560483", "url": "https://glygen.org/publication/PubMed/12560483" } ] }, { "title": "Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation.", "journal": "Nature cell biology", "date": "2008", "authors": "Metzger E, Yin N, Wissmann M, Kunowska N, Fischer K, Friedrichs N, Patnaik D, Higgins JM, Potier N, Scheidtmann KH, Buettner R, Schule R", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "Reactome", "id": "R-HSA-5625886", "url": "https://www.reactome.org/PathwayBrowser/#R-HSA-5625886" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "18066052", "url": "https://glygen.org/publication/PubMed/18066052" } ] }, { "title": "PKM2 phosphorylates histone H3 and promotes gene transcription and tumorigenesis.", "journal": "Cell", "date": "2012", "authors": "Yang W, Xia Y, Hawke D, Li X, Liang J, Xing D, Aldape K, Hunter T, Alfred Yung WK, Lu Z", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "22901803", "url": "https://glygen.org/publication/PubMed/22901803" } ] } ], "crossref": [ { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18243098", "url": "https://glygen.org/publication/PubMed/18243098", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "12560483", "url": "https://glygen.org/publication/PubMed/12560483", "database": "PubMed", "categories": [ "Other" ] }, { "id": "18066052", "url": "https://glygen.org/publication/PubMed/18066052", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22901803", "url": "https://glygen.org/publication/PubMed/22901803", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MARTKQTARKS", "down_seq": "GGKAPRKQLATKAARKSAPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O14757-1", "kinase_gene_name": "CHEK1", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "18243098", "url": "https://glygen.org/publication/PubMed/18243098" } ], "site_lbl": "Thr12" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by PKC", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "12560483", "url": "https://glygen.org/publication/PubMed/12560483" }, { "database": "PubMed", "id": "18066052", "url": "https://glygen.org/publication/PubMed/18066052" }, { "database": "PubMed", "id": "22901803", "url": "https://glygen.org/publication/PubMed/22901803" } ], "site_lbl": "Thr12" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 5, "direction": "downstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "P84243-1.32.32", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P84243-1.29.29", "start_pos": 29, "end_pos": 29, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "MSK activation and physiological roles.", "journal": "Frontiers in bioscience : a journal and virtual library", "date": "2008", "authors": "Arthur JS", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "18508628", "url": "https://glygen.org/publication/PubMed/18508628" } ] }, { "title": "Identification of a novel phosphorylation site on histone H3 coupled with mitotic chromosome condensation.", "journal": "The Journal of biological chemistry", "date": "1999", "authors": "Goto H, Tomono Y, Ajiro K, Kosako H, Fujita M, Sakurai M, Okawa K, Iwamatsu A, Okigaki T, Takahashi T, Inagaki M", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" } ] }, { "title": "MAP kinases mediate UVB-induced phosphorylation of histone H3 at serine 28.", "journal": "The Journal of biological chemistry", "date": "2001", "authors": "Zhong S, Zhang Y, Jansen C, Goto H, Inagaki M, Dong Z", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "11278789", "url": "https://glygen.org/publication/PubMed/11278789" } ] }, { "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": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "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": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" } ] }, { "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": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" } ] }, { "title": "Aurora-B phosphorylates Histone H3 at serine28 with regard to the mitotic chromosome condensation.", "journal": "Genes to cells : devoted to molecular & cellular mechanisms", "date": "2002", "authors": "Goto H, Yasui Y, Nigg EA, Inagaki M", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "11856369", "url": "https://glygen.org/publication/PubMed/11856369" } ] }, { "title": "Histone code pathway involving H3 S28 phosphorylation and K27 acetylation activates transcription and antagonizes polycomb silencing.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2011", "authors": "Lau PN, Cheung P", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "21282660", "url": "https://glygen.org/publication/PubMed/21282660" } ] }, { "title": "The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment.", "journal": "Genes & development", "date": "2005", "authors": "Dai J, Sultan S, Taylor SS, Higgins JM", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610" } ] }, { "title": "Phosphorylation of Ser28 in histone H3 mediated by mixed lineage kinase-like mitogen-activated protein triple kinase alpha.", "journal": "The Journal of biological chemistry", "date": "2005", "authors": "Choi HS, Choi BY, Cho YY, Zhu F, Bode AM, Dong Z", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15684425", "url": "https://glygen.org/publication/PubMed/15684425" } ] }, { "title": "Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2005", "authors": "Hake SB, Garcia BA, Kauer M, Baker SP, Shabanowitz J, Hunt DF, Allis CD", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689" } ] }, { "title": "Modifications of human histone H3 variants during mitosis.", "journal": "Biochemistry", "date": "2005", "authors": "Garcia BA, Barber CM, Hake SB, Ptak C, Turner FB, Busby SA, Shabanowitz J, Moran RG, Allis CD, Hunt DF", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ] } ], "crossref": [ { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "18508628", "url": "https://glygen.org/publication/PubMed/18508628", "database": "PubMed", "categories": [ "Other" ] }, { "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11278789", "url": "https://glygen.org/publication/PubMed/11278789", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "11856369", "url": "https://glygen.org/publication/PubMed/11856369", "database": "PubMed", "categories": [ "Other" ] }, { "id": "21282660", "url": "https://glygen.org/publication/PubMed/21282660", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15684425", "url": "https://glygen.org/publication/PubMed/15684425", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RKSTGGKAPRKQLATKAARK", "down_seq": "APSTGGVKKPHRYRPGTVAL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O75582-1", "kinase_gene_name": "RPS6KA5", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "18508628", "url": "https://glygen.org/publication/PubMed/18508628" } ], "site_lbl": "Ser29" }, { "kinase_uniprot_canonical_ac": "P17612-1", "kinase_gene_name": "PRKACA", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" } ], "site_lbl": "Ser29" }, { "kinase_uniprot_canonical_ac": "P45984-1", "kinase_gene_name": "MAPK9", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "11278789", "url": "https://glygen.org/publication/PubMed/11278789" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser29" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine; alternate; by AURKB, AURKC and RPS6KA5", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" }, { "database": "PubMed", "id": "19007248", "url": "https://glygen.org/publication/PubMed/19007248" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "PubMed", "id": "11856369", "url": "https://glygen.org/publication/PubMed/11856369" }, { "database": "PubMed", "id": "21282660", "url": "https://glygen.org/publication/PubMed/21282660" }, { "database": "PubMed", "id": "10464286", "url": "https://glygen.org/publication/PubMed/10464286" }, { "database": "PubMed", "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610" }, { "database": "PubMed", "id": "15684425", "url": "https://glygen.org/publication/PubMed/15684425" }, { "database": "PubMed", "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689" }, { "database": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ], "site_lbl": "Ser29" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 17, "direction": "downstream", "id": "P84243-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P84243-1.33.33", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P84243-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P84243-1.46.46", "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": 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": 12 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P84243-1.32.32", "start_pos": 32, "end_pos": 32, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Modifications of human histone H3 variants during mitosis.", "journal": "Biochemistry", "date": "2005", "authors": "Garcia BA, Barber CM, Hake SB, Ptak C, Turner FB, Busby SA, Shabanowitz J, Moran RG, Allis CD, Hunt DF", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ] }, { "title": "Serine 31 phosphorylation of histone variant H3.3 is specific to regions bordering centromeres in metaphase chromosomes.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2005", "authors": "Hake SB, Garcia BA, Kauer M, Baker SP, Shabanowitz J, Hunt DF, Allis CD", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088", "database": "PubMed", "categories": [ "Other" ] }, { "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TGGKAPRKQLATKAARKSAP", "down_seq": "TGGVKKPHRYRPGTVALREI", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" }, { "database": "PubMed", "id": "15851689", "url": "https://glygen.org/publication/PubMed/15851689" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "site_lbl": "Ser32" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P84243-1.12.12", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.33.33", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "upstream", "id": "P84243-1.46.46", "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": "P84243-1.42.42", "start_pos": 42, "end_pos": 42, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "JAK2 phosphorylates histone H3Y41 and excludes HP1alpha from chromatin.", "journal": "Nature", "date": "2009", "authors": "Dawson MA, Bannister AJ, Gottgens B, Foster SD, Bartke T, Green AR, Kouzarides T", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "19783980", "url": "https://glygen.org/publication/PubMed/19783980" } ] } ], "crossref": [ { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19783980", "url": "https://glygen.org/publication/PubMed/19783980", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "ATKAARKSAPSTGGVKKPHR", "down_seq": "RPGTVALREIRRYQKSTELL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "O60674-1", "kinase_gene_name": "JAK2", "residue": "Tyr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "19783980", "url": "https://glygen.org/publication/PubMed/19783980" } ], "site_lbl": "Tyr42" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Tyr", "comment": "Phosphotyrosine", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "19783980", "url": "https://glygen.org/publication/PubMed/19783980" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "site_lbl": "Tyr42" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "P84243-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "P84243-1.33.33", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "P84243-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P84243-1.46.46", "categories": [ "phosphorylation_flag" ] }, { "distance": 16, "direction": "upstream", "id": "P84243-1.58.58", "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": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "P84243-1.46.46", "start_pos": 46, "end_pos": 46, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of histone H3 Thr-45 is linked to apoptosis.", "journal": "The Journal of biological chemistry", "date": "2009", "authors": "Hurd PJ, Bannister AJ, Halls K, Dawson MA, Vermeulen M, Olsen JV, Ismail H, Somers J, Mann M, Owen-Hughes T, Gout I, Kouzarides T", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "19363025", "url": "https://glygen.org/publication/PubMed/19363025" } ] } ], "crossref": [ { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "19363025", "url": "https://glygen.org/publication/PubMed/19363025", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "ARKSAPSTGGVKKPHRYRPG", "down_seq": "VALREIRRYQKSTELLIRKL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "", "evidence": [ { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "19363025", "url": "https://glygen.org/publication/PubMed/19363025" } ], "site_lbl": "Thr46" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P84243-1.29.29", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P84243-1.32.32", "categories": [ "phosphorylation_flag" ] }, { "distance": 13, "direction": "downstream", "id": "P84243-1.33.33", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "P84243-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "upstream", "id": "P84243-1.58.58", "categories": [ "phosphorylation_flag" ] }, { "distance": 18, "direction": "upstream", "id": "P84243-1.64.64", "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": "P84243-1.4.4", "start_pos": 4, "end_pos": 4, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment.", "journal": "Genes & development", "date": "2005", "authors": "Dai J, Sultan S, Taylor SS, Higgins JM", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610" } ] }, { "title": "Phosphorylation of histone H3 at Thr3 is part of a combinatorial pattern that marks and configures mitotic chromatin.", "journal": "Journal of cell science", "date": "2009", "authors": "Markaki Y, Christogianni A, Politou AS, Georgatos SD", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "19622635", "url": "https://glygen.org/publication/PubMed/19622635" } ] }, { "title": "Histone H3 Thr-3 phosphorylation by Haspin positions Aurora B at centromeres in mitosis.", "journal": "Science (New York, N.Y.)", "date": "2010", "authors": "Wang F, Dai J, Daum JR, Niedzialkowska E, Banerjee B, Stukenberg PT, Gorbsky GJ, Higgins JM", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20705812", "url": "https://glygen.org/publication/PubMed/20705812" } ] }, { "title": "Two histone marks establish the inner centromere and chromosome bi-orientation.", "journal": "Science (New York, N.Y.)", "date": "2010", "authors": "Yamagishi Y, Honda T, Tanno Y, Watanabe Y", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20929775", "url": "https://glygen.org/publication/PubMed/20929775" } ] }, { "title": "A phospho/methyl switch at histone H3 regulates TFIID association with mitotic chromosomes.", "journal": "The EMBO journal", "date": "2010", "authors": "Varier RA, Outchkourov NS, de Graaf P, van Schaik FM, Ensing HJ, Wang F, Higgins JM, Kops GJ, Timmers HT", "evidence": [ { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20953165", "url": "https://glygen.org/publication/PubMed/20953165" } ] }, { "title": "Modifications of human histone H3 variants during mitosis.", "journal": "Biochemistry", "date": "2005", "authors": "Garcia BA, Barber CM, Hake SB, Ptak C, Turner FB, Busby SA, Shabanowitz J, Moran RG, Allis CD, Hunt DF", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610", "database": "PubMed", "categories": [ "Other" ] }, { "id": "19622635", "url": "https://glygen.org/publication/PubMed/19622635", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20705812", "url": "https://glygen.org/publication/PubMed/20705812", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20929775", "url": "https://glygen.org/publication/PubMed/20929775", "database": "PubMed", "categories": [ "Other" ] }, { "id": "20953165", "url": "https://glygen.org/publication/PubMed/20953165", "database": "PubMed", "categories": [ "Other" ] }, { "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MAR", "down_seq": "KQTARKSTGGKAPRKQLATK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by HASPIN and VRK1", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "15681610", "url": "https://glygen.org/publication/PubMed/15681610" }, { "database": "PubMed", "id": "19622635", "url": "https://glygen.org/publication/PubMed/19622635" }, { "database": "PubMed", "id": "20705812", "url": "https://glygen.org/publication/PubMed/20705812" }, { "database": "PubMed", "id": "20929775", "url": "https://glygen.org/publication/PubMed/20929775" }, { "database": "PubMed", "id": "20953165", "url": "https://glygen.org/publication/PubMed/20953165" }, { "database": "PubMed", "id": "16185088", "url": "https://glygen.org/publication/PubMed/16185088" } ], "site_lbl": "Thr4" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.7.7", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 8, "direction": "upstream", "id": "P84243-1.12.12", "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": "P84243-1.58.58", "start_pos": 58, "end_pos": 58, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers.", "journal": "Cell", "date": "2010", "authors": "Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20850016", "url": "https://glygen.org/publication/PubMed/20850016" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20850016", "url": "https://glygen.org/publication/PubMed/20850016", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KPHRYRPGTVALREIRRYQK", "down_seq": "TELLIRKLPFQRLVREIAQD", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "20850016", "url": "https://glygen.org/publication/PubMed/20850016" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "site_lbl": "Ser58" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "P84243-1.42.42", "categories": [ "phosphorylation_flag" ] }, { "distance": 15, "direction": "downstream", "id": "P84243-1.43.43", "categories": [ "mutagenesis_flag" ] }, { "distance": 12, "direction": "downstream", "id": "P84243-1.46.46", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P84243-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "P84243-1.67.67", "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": "P84243-1.7.7", "start_pos": 7, "end_pos": 7, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Phosphorylation of histone H3T6 by PKCbeta(I) controls demethylation at histone H3K4.", "journal": "Nature", "date": "2010", "authors": "Metzger E, Imhof A, Patel D, Kahl P, Hoffmeyer K, Friedrichs N, Muller JM, Greschik H, Kirfel J, Ji S, Kunowska N, Beisenherz-Huss C, Gunther T, Buettner R, Schule R", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20228790", "url": "https://glygen.org/publication/PubMed/20228790" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243", "database": "PRO", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "20228790", "url": "https://glygen.org/publication/PubMed/20228790", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "MARTKQ", "down_seq": "ARKSTGGKAPRKQLATKAAR", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by PKC", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PRO", "id": "P84243", "url": "https://proconsortium.org/cgi-bin/entry_pro?id=P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "20228790", "url": "https://glygen.org/publication/PubMed/20228790" } ], "site_lbl": "Thr7" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "P84243-1.3.3", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "P84243-1.4.4", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "P84243-1.5.5", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "P84243-1.6.6", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "P84243-1.10.10", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "P84243-1.11.11", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "P84243-1.12.12", "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": "P84243-1.81.81", "start_pos": 81, "end_pos": 81, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers.", "journal": "Cell", "date": "2010", "authors": "Vermeulen M, Eberl HC, Matarese F, Marks H, Denissov S, Butter F, Lee KK, Olsen JV, Hyman AA, Stunnenberg HG, Mann M", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20850016", "url": "https://glygen.org/publication/PubMed/20850016" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20850016", "url": "https://glygen.org/publication/PubMed/20850016", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "LLIRKLPFQRLVREIAQDFK", "down_seq": "DLRFQSAAIGALQEASEAYL", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "20850016", "url": "https://glygen.org/publication/PubMed/20850016" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "site_lbl": "Thr81" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "P84243-1.64.64", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "P84243-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "P84243-1.87.87", "categories": [ "phosphorylation_flag" ] }, { "distance": 17, "direction": "upstream", "id": "P84243-1.98.98", "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": "P84243-1.87.87", "start_pos": 87, "end_pos": 87, "uniprot_canonical_ac": "P84243-1", "length": 136, "uniprot_id": "H33_HUMAN", "protein_name": "Histone H3.3", "refseq_ac": "NP_002098", "refseq_name": "histone H3.3", "gene_name": "H3-3A; H3-3B", "gene_names_uniprotkb": "H3-3A; H3-3B; H3.3A; H3.3B; H3F3A; H3F3B; H3F3; PP781", "gene_names_refseq": "BRYLIB1; H3-3A; H3.3A; H3F3A; H3F3", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" } ], "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": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "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": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569", "database": "PubMed", "categories": [ "Other" ] }, { "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243", "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": "PFQRLVREIAQDFKTDLRFQ", "down_seq": "AAIGALQEASEAYLVGLFED", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "P84243", "url": "https://www.uniprot.org/uniprotkb/P84243" }, { "database": "PubMed", "id": "24275569", "url": "https://glygen.org/publication/PubMed/24275569" }, { "database": "iPTMnet", "id": "P84243", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/P84243" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ], "site_lbl": "Ser87" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "11", "end_pos": "11" }, { "start_pos": "33", "end_pos": "33" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "106", "end_pos": "107" }, { "start_pos": "43", "end_pos": "43" }, { "start_pos": "6", "end_pos": "6" } ] }, { "type": "snv", "site_list": [ { "start_pos": "35", "end_pos": "35" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "10", "end_pos": "10" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "130", "end_pos": "130" }, { "start_pos": "33", "end_pos": "33" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "5", "end_pos": "5" }, { "start_pos": "64", "end_pos": "64" }, { "start_pos": "67", "end_pos": "67" }, { "start_pos": "98", "end_pos": "98" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "108", "end_pos": "108" }, { "start_pos": "11", "end_pos": "11" }, { "start_pos": "12", "end_pos": "12" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "32", "end_pos": "32" }, { "start_pos": "42", "end_pos": "42" }, { "start_pos": "46", "end_pos": "46" }, { "start_pos": "4", "end_pos": "4" }, { "start_pos": "58", "end_pos": "58" }, { "start_pos": "7", "end_pos": "7" }, { "start_pos": "81", "end_pos": "81" }, { "start_pos": "87", "end_pos": "87" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "P84243-1.67.67", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "P84243-1.81.81", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "P84243-1.98.98", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P84243-1.106.107", "categories": [ "mutagenesis_flag" ] }, { "distance": 19, "direction": "upstream", "id": "P84243-1.106.106", "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": "Q9BQ15-1.51.51", "start_pos": 51, "end_pos": 51, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "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": "rs957219985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs957219985", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs957219985", "url": "https://www.ncbi.nlm.nih.gov/snp/rs957219985#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "KTKDGHEVRTCKVADKTGSI", "down_seq": "ISVWDDVGNLIQPGDIIRLT", "glycosylation": [ { "glytoucan_ac": "G63198FP", "type": "N-linked", "subtype": "", "prediction_tool_list": [], "site_category": "reported_with_glycan", "site_category_dict": { "reported_with_glycan": true }, "site_seq": "TGSINISVWDDVGNLIQPGDIIR", "relation": "attached", "comment": "", "icn3d_view": {}, "start_aa": "Asn", "end_aa": "Asn", "residue": "Asn", "site_lbl": "Asn51", "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": "rs957219985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs957219985" }, { "id": "rs957219985", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs957219985#frequency_tab" } ], "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": "12", "chr_pos": "56225445", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N51", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "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": 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": "Q9BQ15-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "O-GlcNAc Transferase Recognizes Protein Substrates Using an Asparagine Ladder in the Tetratricopeptide Repeat (TPR) Superhelix.", "journal": "Journal of the American Chemical Society", "date": "2018", "authors": "Levine ZG, Fan C, Melicher MS, Orman M, Benjamin T, Walker S", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q9BQ15", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BQ15" } ], "reference": [ { "type": "PubMed", "id": "29485866", "url": "https://glygen.org/publication/PubMed/29485866" } ] } ], "crossref": [ { "id": "29485866", "url": "https://glygen.org/publication/PubMed/29485866", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BQ15", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BQ15", "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": "29485866", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29485866" }, { "id": "Q9BQ15", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q9BQ15" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "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": "Q9BQ15-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Single-stranded DNA-binding protein hSSB1 is critical for genomic stability.", "journal": "Nature", "date": "2008", "authors": "Richard DJ, Bolderson E, Cubeddu L, Wadsworth RI, Savage K, Sharma GG, Nicolette ML, Tsvetanov S, McIlwraith MJ, Pandita RK, Takeda S, Hay RT, Gautier J, West SC, Paull TT, Pandita TK, White MF, Khanna KK", "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" }, { "database": "RefSeq", "id": "NP_076973", "url": "https://www.ncbi.nlm.nih.gov/protein/NP_076973" }, { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" } ], "reference": [ { "type": "PubMed", "id": "18449195", "url": "https://glygen.org/publication/PubMed/18449195" } ] }, { "title": "FBXL5-mediated degradation of single-stranded DNA-binding protein hSSB1 controls DNA damage response.", "journal": "Nucleic acids research", "date": "2014", "authors": "Chen ZW, Liu B, Tang NW, Xu YH, Ye XY, Li ZM, Niu XM, Shen SP, Lu S, Xu L", "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" }, { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" } ], "reference": [ { "type": "PubMed", "id": "25249620", "url": "https://glygen.org/publication/PubMed/25249620" } ] }, { "title": "hSSB1 phosphorylation is dynamically regulated by DNA-PK and PPP-family protein phosphatases.", "journal": "DNA repair", "date": "2017", "authors": "Ashton NW, Paquet N, Shirran SL, Bolderson E, Kariawasam R, Touma C, Fallahbaghery A, Gamsjaeger R, Cubeddu L, Botting C, Pollock PM, O'Byrne KJ, Richard DJ", "evidence": [ { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" } ], "reference": [ { "type": "PubMed", "id": "28448822", "url": "https://glygen.org/publication/PubMed/28448822" } ] } ], "crossref": [ { "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18449195", "url": "https://glygen.org/publication/PubMed/18449195", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "25249620", "url": "https://glygen.org/publication/PubMed/25249620", "database": "PubMed", "categories": [ "Other" ] }, { "id": "28448822", "url": "https://glygen.org/publication/PubMed/28448822", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EFCMVYSEVPNFSEPNPEYS", "down_seq": "QQAPNKAVQNDSNPSASQPT", "mutagenesis": [ { "sequence_org": "T", "sequence_mut": "A", "comment": "Loss of phosphorylation by ATM.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" }, { "database": "PubMed", "id": "18449195", "url": "https://glygen.org/publication/PubMed/18449195" } ] }, { "sequence_org": "T", "sequence_mut": "E", "comment": "Enhances ATM-dependent signaling.", "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" }, { "database": "PubMed", "id": "18449195", "url": "https://glygen.org/publication/PubMed/18449195" } ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "Q13315-1", "kinase_gene_name": "ATM", "residue": "Thr", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" }, { "database": "PubMed", "id": "18449195", "url": "https://glygen.org/publication/PubMed/18449195" } ], "site_lbl": "Thr117" }, { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine; by ATM", "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" }, { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" }, { "database": "PubMed", "id": "25249620", "url": "https://glygen.org/publication/PubMed/25249620" }, { "database": "PubMed", "id": "28448822", "url": "https://glygen.org/publication/PubMed/28448822" }, { "database": "PubMed", "id": "18449195", "url": "https://glygen.org/publication/PubMed/18449195" } ], "site_lbl": "Thr117" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "mutagenesis_flag", "phosphorylation_flag" ], "glycosylation": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q9BQ15-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q9BQ15-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q9BQ15-1.134.134", "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": 3 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q9BQ15-1.124.124", "start_pos": 124, "end_pos": 124, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1009605853", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009605853", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1009605853", "url": "https://www.ensembl.org/id/rs1009605853", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q9BQ15", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EVPNFSEPNPEYSTQQAPNK", "down_seq": "VQNDSNPSASQPTTGPSAAS", "snv": [ { "evidence": [ { "id": "rs1009605853", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1009605853" }, { "id": "rs1009605853", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1009605853" } ], "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": "12", "chr_pos": "56226258", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A124", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q9BQ15", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "56226259", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A124", "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": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q9BQ15-1.117.117", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q9BQ15-1.131.131", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q9BQ15-1.134.134", "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", "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": "Q9BQ15-1.131.131", "start_pos": 131, "end_pos": 131, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQ15", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1462861975", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1462861975", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1462861975", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1462861975#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1462861975", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1462861975", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1355781936", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355781936", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1355781936", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1355781936#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1355781936", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355781936", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1355781936", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1355781936", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PNPEYSTQQAPNKAVQNDSN", "down_seq": "SASQPTTGPSAASPASENQN", "snv": [ { "evidence": [ { "id": "Q9BQ15", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2670", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NLS).", "chr_id": "12", "chr_pos": "56226375", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P131", "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": "rs1462861975", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1462861975" }, { "id": "rs1462861975", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1462861975#frequency_tab" }, { "id": "rs1462861975", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1462861975" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "R", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NPS->NRS).", "chr_id": "12", "chr_pos": "56226375", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P131", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1355781936", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355781936" }, { "id": "rs1355781936", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1355781936#frequency_tab" }, { "id": "rs1355781936", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355781936" }, { "id": "rs1355781936", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1355781936" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NPS->NSS).", "chr_id": "12", "chr_pos": "56226374", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P131", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs1355781936", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1355781936" }, { "id": "rs1355781936", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1355781936#frequency_tab" }, { "id": "rs1355781936", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1355781936" } ], "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": "12", "chr_pos": "56226374", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "P131", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q9BQ15-1.117.117", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q9BQ15-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q9BQ15-1.134.134", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": "Q9BQ15-1.172.172", "start_pos": 172, "end_pos": 172, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQ15", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GNGLSAPPGPGGGPHPPHTP", "down_seq": "HPPSTRITRSQPNHTPAGPP", "snv": [ { "evidence": [ { "id": "Q9BQ15", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "56229091", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S172", "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: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": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q9BQ15-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q9BQ15-1.191.191", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQ15-1.173.173", "start_pos": 173, "end_pos": 173, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQ15", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "H", "start_aa": "H", "up_seq": "NGLSAPPGPGGGPHPPHTPS", "down_seq": "PPSTRITRSQPNHTPAGPPG", "snv": [ { "evidence": [ { "id": "Q9BQ15", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15" } ], "glycoeffect": [], "subjects_tested": "1906", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "H", "sequence_mut": "P", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "12", "chr_pos": "56229095", "ref_nt": "A", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "H173", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q9BQ15-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q9BQ15-1.191.191", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQ15-1.191.191", "start_pos": 191, "end_pos": 191, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQ15", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PSHPPSTRITRSQPNHTPAG", "down_seq": "PGPSSNPVSNGKETRRSSKR", "snv": [ { "evidence": [ { "id": "Q9BQ15", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "12", "chr_pos": "56229149", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "P191", "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": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q9BQ15-1.172.172", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q9BQ15-1.173.173", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q9BQ15-1.202.202", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q9BQ15-1.202.202", "start_pos": 202, "end_pos": 202, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q9BQ15", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "SQPNHTPAGPPGPSSNPVSN", "down_seq": "KETRRSSKR", "snv": [ { "evidence": [ { "id": "Q9BQ15", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q9BQ15" } ], "glycoeffect": [], "subjects_tested": "92", "subjects_positive": "1", "frequency": "1.1", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: patient freq. (1.1%).", "chr_id": "12", "chr_pos": "56229181", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G202", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q9BQ15-1.191.191", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q9BQ15-1.134.134", "start_pos": 134, "end_pos": 134, "uniprot_canonical_ac": "Q9BQ15-1", "length": 211, "uniprot_id": "SOSB1_HUMAN", "protein_name": "SOSS complex subunit B1", "refseq_ac": "NP_076973", "refseq_name": "SOSS complex subunit B1", "gene_name": "NABP2", "gene_names_uniprotkb": "NABP2; LP3587; OBFC2B; SSB1", "gene_names_refseq": "NABP2; OBFC2B; SOSS-B1; SSB1; hSSB1", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q9BQ15", "url": "https://www.uniprot.org/uniprotkb/Q9BQ15" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "hSSB1 phosphorylation is dynamically regulated by DNA-PK and PPP-family protein phosphatases.", "journal": "DNA repair", "date": "2017", "authors": "Ashton NW, Paquet N, Shirran SL, Bolderson E, Kariawasam R, Touma C, Fallahbaghery A, Gamsjaeger R, Cubeddu L, Botting C, Pollock PM, O'Byrne KJ, Richard DJ", "evidence": [ { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" } ], "reference": [ { "type": "PubMed", "id": "28448822", "url": "https://glygen.org/publication/PubMed/28448822" } ] } ], "crossref": [ { "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15", "database": "iPTMnet", "categories": [ "Other" ] }, { "id": "28448822", "url": "https://glygen.org/publication/PubMed/28448822", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "EYSTQQAPNKAVQNDSNPSA", "down_seq": "QPTTGPSAASPASENQNGNG", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "", "evidence": [ { "database": "iPTMnet", "id": "Q9BQ15", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q9BQ15" }, { "database": "PubMed", "id": "28448822", "url": "https://glygen.org/publication/PubMed/28448822" } ], "site_lbl": "Ser134" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "51", "end_pos": "51" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "117", "end_pos": "117" } ] }, { "type": "snv", "site_list": [ { "start_pos": "124", "end_pos": "124" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "172", "end_pos": "172" }, { "start_pos": "173", "end_pos": "173" }, { "start_pos": "191", "end_pos": "191" }, { "start_pos": "202", "end_pos": "202" }, { "start_pos": "51", "end_pos": "51" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "117", "end_pos": "117" }, { "start_pos": "134", "end_pos": "134" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q9BQ15-1.117.117", "categories": [ "mutagenesis_flag", "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q9BQ15-1.124.124", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q9BQ15-1.131.131", "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": "Q6W2J9-1.106.106", "start_pos": 106, "end_pos": 106, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs955055636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955055636", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs955055636", "url": "https://www.ncbi.nlm.nih.gov/snp/rs955055636#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs955055636", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955055636", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs2147275510", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147275510", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147275510", "url": "https://www.ensembl.org/id/rs2147275510", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "GNIVYSSLCGLGSEKGREAA", "down_seq": "STLGGLGFSSERNPEMQFKP", "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": "Thr106", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "rs955055636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955055636" }, { "id": "rs955055636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs955055636#frequency_tab" }, { "id": "rs955055636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955055636" } ], "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": "X", "chr_pos": "40075030", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2147275510", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147275510" }, { "id": "rs2147275510", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147275510" } ], "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": "X", "chr_pos": "40075029", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2147275510", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147275510" }, { "id": "rs2147275510", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147275510" } ], "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": "X", "chr_pos": "40075029", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs955055636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs955055636" }, { "id": "rs955055636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs955055636#frequency_tab" }, { "id": "rs955055636", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs955055636" } ], "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": "X", "chr_pos": "40075030", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2147275510", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147275510" }, { "id": "rs2147275510", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147275510" } ], "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": "X", "chr_pos": "40075029", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T106", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.90.90", "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": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 5 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.1691.1691", "start_pos": 1691, "end_pos": 1691, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1409439985", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1409439985", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1409439985", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1409439985#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1409439985", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1409439985", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1409439985", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1409439985", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "KKLKMSSRIFRCNFPNVEIV", "down_seq": "IAEAEFYRQVSASLLFSCSK", "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": "Thr1691", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1409439985", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1409439985" }, { "id": "rs1409439985", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1409439985#frequency_tab" }, { "id": "rs1409439985", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1409439985" }, { "id": "rs1409439985", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1409439985" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "23", "chr_pos": "40052306", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T1691", "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", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.1681.1681", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.1706.1706", "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": 1 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 1 }, { "field": "exact_sites", "count": 0 }, { "field": "fuzzy_sites", "count": 1 }, { "field": "fuzzy_o_linked_sites", "count": 1 }, { "field": "fuzzy_o_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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] } ], "crossref": [ { "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "SYSLAQPLYSPVCTNGERFL", "down_seq": "LPPPHYVGPHIPSSLASPMR", "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": "Y", "relation": "attached", "comment": "O-GlcNAcylation", "icn3d_view": {}, "start_aa": "Tyr", "end_aa": "Tyr", "residue": "Tyr", "site_lbl": "Tyr246", "evidence": [ { "id": "39531497", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39531497" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.259.259", "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": "Q6W2J9-1.365.365", "start_pos": 365, "end_pos": 365, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260", "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": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LPTQPAADTYSEFHKHYARI", "down_seq": "TSPSVALSKPYMTVSSEFPA", "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": "Ser365", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "23", "chr_pos": "40074252", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S365", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser365" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.366.366", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.367.367", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.369.369", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.373.373", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.378.378", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "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": "Q6W2J9-1.366.366", "start_pos": 366, "end_pos": 366, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1307035202", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1307035202", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1307035202", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1307035202#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1307035202", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1307035202", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs779192905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779192905", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs779192905", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779192905", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs779192905", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779192905#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs779192905", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779192905", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PTQPAADTYSEFHKHYARIS", "down_seq": "SPSVALSKPYMTVSSEFPAA", "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": "Thr366", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1307035202", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1307035202" }, { "id": "rs1307035202", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1307035202#frequency_tab" }, { "id": "rs1307035202", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1307035202" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "23", "chr_pos": "40074250", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T366", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] }, { "evidence": [ { "id": "rs779192905", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779192905" }, { "id": "rs779192905", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs779192905" }, { "id": "rs779192905", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs779192905#frequency_tab" }, { "id": "rs779192905", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs779192905" } ], "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": "X", "chr_pos": "40074249", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T366", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.365.365", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.367.367", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.369.369", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.373.373", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6W2J9-1.378.378", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.367.367", "start_pos": 367, "end_pos": 367, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2147252355", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147252355", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147252355", "url": "https://www.ensembl.org/id/rs2147252355", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TQPAADTYSEFHKHYARIST", "down_seq": "PSVALSKPYMTVSSEFPAAR", "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": "Ser367", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "rs2147252355", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147252355" }, { "id": "rs2147252355", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147252355" } ], "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": "X", "chr_pos": "40074246", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S367", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser367" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.365.365", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.366.366", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.369.369", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.373.373", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.378.378", "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": "Q6W2J9-1.369.369", "start_pos": 369, "end_pos": 369, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2147252234", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147252234", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147252234", "url": "https://www.ensembl.org/id/rs2147252234", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PAADTYSEFHKHYARISTSP", "down_seq": "VALSKPYMTVSSEFPAARLS", "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": "Ser369", "evidence": [ { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "rs2147252234", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147252234" }, { "id": "rs2147252234", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147252234" } ], "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": "X", "chr_pos": "40074240", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S369", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.365.365", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.366.366", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.367.367", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.373.373", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.378.378", "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": "Q6W2J9-1.373.373", "start_pos": 373, "end_pos": 373, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1443453511", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443453511", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1443453511", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1443453511#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1443453511", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443453511", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1443453511", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1443453511", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TYSEFHKHYARISTSPSVAL", "down_seq": "KPYMTVSSEFPAARLSNGKY", "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": "Ser373", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "35705054", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35705054" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "2617", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "23", "chr_pos": "40074228", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S373", "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" ] }, { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1443453511", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1443453511" }, { "id": "rs1443453511", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1443453511#frequency_tab" }, { "id": "rs1443453511", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1443453511" }, { "id": "rs1443453511", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1443453511" } ], "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: o-glyco-site-loss (S->L).", "chr_id": "23", "chr_pos": "40074228", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S373", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.365.365", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.366.366", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.367.367", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.369.369", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.378.378", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_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": 21 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.378.378", "start_pos": 378, "end_pos": 378, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] } ], "crossref": [ { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1935655295", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935655295", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1935655295", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1935655295#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "HKHYARISTSPSVALSKPYM", "down_seq": "VSSEFPAARLSNGKYPKAPE", "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": "Thr378", "evidence": [ { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "T", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (T->A).", "chr_id": "23", "chr_pos": "40074214", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "T378", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "rs1935655295", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935655295" }, { "id": "rs1935655295", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1935655295#frequency_tab" } ], "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": "X", "chr_pos": "40074213", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T378", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.365.365", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6W2J9-1.366.366", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.367.367", "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.369.369", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.373.373", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.453.453", "start_pos": 453, "end_pos": 453, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TKDVTDKPLDLSSKVVDVDA", "down_seq": "KADHMKKMAPTVLVHSRAGS", "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": "Ser453", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.442.442", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.555.555", "start_pos": 555, "end_pos": 555, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "AIPQQRSSSCPRMGGTDAVI", "down_seq": "NVSGSVSSAGRPASASPAPN", "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": "Thr555", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag" ], "mutagenesis": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.560.560", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.563.563", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.570.570", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.560.560", "start_pos": 560, "end_pos": 560, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs2147236990", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147236990", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147236990", "url": "https://www.ensembl.org/id/rs2147236990", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RSSSCPRMGGTDAVITNVSG", "down_seq": "VSSAGRPASASPAPNANADG", "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": "Ser560", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "rs2147236990", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147236990" }, { "id": "rs2147236990", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147236990" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "*", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (S->*).", "chr_id": "X", "chr_pos": "40073667", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S560", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->L).", "chr_id": "23", "chr_pos": "40073667", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S560", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.555.555", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.563.563", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.570.570", "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", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.563.563", "start_pos": 563, "end_pos": 563, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs1935608636", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935608636", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1935608636", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1935608636#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SCPRMGGTDAVITNVSGSVS", "down_seq": "AGRPASASPAPNANADGTKT", "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": "Ser563", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "rs1935608636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935608636" }, { "id": "rs1935608636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1935608636#frequency_tab" } ], "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": "X", "chr_pos": "40073658", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S563", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1935608636", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935608636" }, { "id": "rs1935608636", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1935608636#frequency_tab" } ], "glycoeffect": [ "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: o-glyco-site-loss (S->N).", "chr_id": "23", "chr_pos": "40073658", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S563", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.555.555", "categories": [ "glycosylation_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.560.560", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.570.570", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.581.581", "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", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.586.586", "start_pos": 586, "end_pos": 586, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "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": "rs867271265", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867271265", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs867271265", "url": "https://www.ensembl.org/id/rs867271265", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "RPASASPAPNANADGTKTSR", "down_seq": "SVETTPSVIQHVGQPPATPA", "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": "Ser586", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" }, { "id": "35513511", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35513511" }, { "id": "37541260", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "snv": [ { "evidence": [ { "id": "rs867271265", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs867271265" }, { "id": "rs867271265", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs867271265" } ], "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": "X", "chr_pos": "40073589", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S586", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "R", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->R).", "chr_id": "23", "chr_pos": "40073588", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S586", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.570.570", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.581.581", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.587.587", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.604.604", "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", "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": 22 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.587.587", "start_pos": 587, "end_pos": 587, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PASASPAPNANADGTKTSRS", "down_seq": "VETTPSVIQHVGQPPATPAK", "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": "Ser587", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->Y).", "chr_id": "23", "chr_pos": "40073586", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S587", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.570.570", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.581.581", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.586.586", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.604.604", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.604.604", "start_pos": 604, "end_pos": 604, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "rs762433029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762433029", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs762433029", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762433029", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs762433029", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762433029", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "SRSSVETTPSVIQHVGQPPA", "down_seq": "PAKHSSSTSSKGAKASNPEP", "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": "Thr604", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs762433029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762433029" }, { "id": "rs762433029", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762433029" }, { "id": "rs762433029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762433029" } ], "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": "X", "chr_pos": "40073536", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T604", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs762433029", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762433029" }, { "id": "rs762433029", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs762433029" }, { "id": "rs762433029", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs762433029" } ], "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": "X", "chr_pos": "40073536", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T604", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.586.586", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.587.587", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.609.609", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.611.611", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] } ], "glycosylation_flag": true, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 1 }, { "field": "total_sites", "count": 1 }, { "field": "n_linked_sites", "count": 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": "Q6W2J9-1.636.636", "start_pos": 636, "end_pos": 636, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "rs2147230235", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147230235", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147230235", "url": "https://www.ensembl.org/id/rs2147230235", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2147230235", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2147230235", "database": "COSMIC", "categories": [ "Other" ] }, { "id": "rs2519987858", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2519987858", "database": "dbSNP", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GAKASNPEPSFKANENGLPP", "down_seq": "SIFLSPNEAFRSPPIPYPRS", "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": "Ser636", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "snv": [ { "evidence": [ { "id": "rs2147230235", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147230235" }, { "id": "rs2147230235", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147230235" }, { "id": "rs2147230235", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2147230235" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->I).", "chr_id": "X", "chr_pos": "40073439", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S636", "keywords": [ "ebi", "somatic" ] }, { "evidence": [ { "id": "rs2519987858", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2519987858" } ], "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": "X", "chr_pos": "40073438", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S636", "disease": [ { "disease_id": "DOID:0111809", "recommended_name": { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "syndromic microphthalmia 2", "description": "A syndromic microphthalmia characterized by ocular defects including microphthalmia, microcornea, and congentital cataract; facial dysmorphism including septate nasal cartilage with high nasal bridge; congenital heart defects, most commonly a septal defect; and dental anomalies, most commonly persistent primary teeth and radiculomegaly that has_material_basis_in mutation in the BCL6 corepressor gene on chromosome Xp11." }, "synonyms": [ { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "ANOP2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "MAA2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "MCOPS2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "OFCD syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "oculofaciocardiodental syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "syndromic microphthalmia type 2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "cataract-microphthalmia-radiculomegaly-cardiac septal defect syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "microphthalmia cataracts radiculomegaly and septal heart defects", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "OFCD syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "cataract-microphthalmia-radiculomegaly-cardiac septal defect syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic type 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "oculofaciocardiodental syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "ANOP2 (formerly)", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "MAA2 (formerly)", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "MCOPS2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia cataracts radiculomegaly and septal heart defects", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "syndromic microphthalmia type 2", "description": "" }, { "id": "MIM:300166", "resource": "MIM", "url": "https://www.omim.org/entry/300166", "name": "Microphthalmia, syndromic, 2", "description": "Microphthalmia, syndromic, 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300166", "database": "MIM", "url": "https://www.omim.org/entry/300166" }, { "id": "0111809", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111809" } ] } ], "keywords": [ "ebi", "germline", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.637.637", "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": 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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.637.637", "start_pos": 637, "end_pos": 637, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "database": "O-GlcNAc Atlas", "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "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": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "38253038", "url": "https://glygen.org/publication/PubMed/38253038", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9", "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": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038", "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": "30379171", "url": "https://glygen.org/publication/PubMed/30379171", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842", "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": "35289036", "url": "https://glygen.org/publication/PubMed/35289036", "database": "PubMed", "categories": [ "Other" ] }, { "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207", "database": "PubMed", "categories": [ "Other" ] }, { "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498", "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": "35138101", "url": "https://glygen.org/publication/PubMed/35138101", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://oglcnac.org/atlas/detail/Q6W2J9", "database": "O-GlcNAc Atlas", "categories": [ "Glycoproteomics" ] }, { "id": "rs148052848", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148052848", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148052848", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148052848", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148052848", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148052848#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148052848", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148052848", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AKASNPEPSFKANENGLPPS", "down_seq": "IFLSPNEAFRSPPIPYPRSY", "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": "Ser637", "evidence": [ { "id": "38253038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38253038" }, { "id": "Q6W2J9", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q6W2J9" }, { "id": "29237092", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/29237092" }, { "id": "30620550", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30620550" }, { "id": "39534244", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/39534244" }, { "id": "32574038", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/32574038" }, { "id": "40596516", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40596516" }, { "id": "30059200", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30059200" }, { "id": "30379171", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/30379171" }, { "id": "34846842", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34846842" }, { "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": "35289036", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35289036" }, { "id": "40307207", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/40307207" }, { "id": "23301498", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/23301498" }, { "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": "35138101", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/35138101" }, { "id": "Q6W2J9", "database": "O-GlcNAc Atlas", "url": "https://oglcnac.org/atlas/detail/Q6W2J9" } ] } ], "snv": [ { "evidence": [ { "id": "rs148052848", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148052848" }, { "id": "rs148052848", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148052848" }, { "id": "rs148052848", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148052848#frequency_tab" }, { "id": "rs148052848", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148052848" } ], "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": "X", "chr_pos": "40073436", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S637", "disease": [ { "disease_id": "DOID:0111809", "recommended_name": { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "syndromic microphthalmia 2", "description": "A syndromic microphthalmia characterized by ocular defects including microphthalmia, microcornea, and congentital cataract; facial dysmorphism including septate nasal cartilage with high nasal bridge; congenital heart defects, most commonly a septal defect; and dental anomalies, most commonly persistent primary teeth and radiculomegaly that has_material_basis_in mutation in the BCL6 corepressor gene on chromosome Xp11." }, "synonyms": [ { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "ANOP2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "MAA2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "MCOPS2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "OFCD syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "oculofaciocardiodental syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "syndromic microphthalmia type 2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "cataract-microphthalmia-radiculomegaly-cardiac septal defect syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "microphthalmia cataracts radiculomegaly and septal heart defects", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "OFCD syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "cataract-microphthalmia-radiculomegaly-cardiac septal defect syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic type 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "oculofaciocardiodental syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "ANOP2 (formerly)", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "MAA2 (formerly)", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "MCOPS2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia cataracts radiculomegaly and septal heart defects", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "syndromic microphthalmia type 2", "description": "" }, { "id": "MIM:300166", "resource": "MIM", "url": "https://www.omim.org/entry/300166", "name": "Microphthalmia, syndromic, 2", "description": "Microphthalmia, syndromic, 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300166", "database": "MIM", "url": "https://www.omim.org/entry/300166" }, { "id": "0111809", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111809" } ] } ], "keywords": [ "ebi", "germline", "disease" ] }, { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "F", "comment": "Somatic mutation passed 1 filters: o-glyco-site-loss (S->F).", "chr_id": "23", "chr_pos": "40073436", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S637", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "glycosylation_flag", "snv_flag" ], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.636.636", "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", "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": 20 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.1706.1706", "start_pos": 1706, "end_pos": 1706, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of the polycomb group protein PCGF1 in complex with BCOR reveals basis for binding selectivity of PCGF homologs.", "journal": "Structure (London, England : 1993)", "date": "2013", "authors": "Junco SE, Wang R, Gaipa JC, Taylor AB, Schirf V, Gearhart MD, Bardwell VJ, Demeler B, Hart PJ, Kim CA", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23523425", "url": "https://glygen.org/publication/PubMed/23523425" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23523425", "url": "https://glygen.org/publication/PubMed/23523425", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "L", "start_aa": "L", "up_seq": "NVEIVTIAEAEFYRQVSASL", "down_seq": "FSCSKDLEAFNPESKELLDL", "mutagenesis": [ { "sequence_org": "L", "sequence_mut": "D", "comment": "Slightly inhibits interaction with PCGF1.", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "23523425", "url": "https://glygen.org/publication/PubMed/23523425" } ] }, { "sequence_org": "L", "sequence_mut": "R", "comment": "Slightly inhibits interaction with PCGF1.", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "23523425", "url": "https://glygen.org/publication/PubMed/23523425" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.1691.1691", "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": "Q6W2J9-1.507.507", "start_pos": 507, "end_pos": 507, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer.", "journal": "Molecular cell", "date": "2008", "authors": "Ghetu AF, Corcoran CM, Cerchietti L, Bardwell VJ, Melnick A, Prive GG", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LSPPGNGCAIYRSEIISTAP", "down_seq": "SWVVPGPSPNEENNGKSMSL", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Abolishes interaction with BCL6 and inhibits BCL6 corepression activity; when associated with A-509 and A-511.", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.526.526", "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": "Q6W2J9-1.508.508", "start_pos": 508, "end_pos": 508, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer.", "journal": "Molecular cell", "date": "2008", "authors": "Ghetu AF, Corcoran CM, Cerchietti L, Bardwell VJ, Melnick A, Prive GG", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "SPPGNGCAIYRSEIISTAPS", "down_seq": "WVVPGPSPNEENNGKSMSLK", "mutagenesis": [ { "sequence_org": "S", "sequence_mut": "A", "comment": "Diminishes interaction with BCL6.", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.526.526", "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": "Q6W2J9-1.509.509", "start_pos": 509, "end_pos": 509, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer.", "journal": "Molecular cell", "date": "2008", "authors": "Ghetu AF, Corcoran CM, Cerchietti L, Bardwell VJ, Melnick A, Prive GG", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "PPGNGCAIYRSEIISTAPSS", "down_seq": "VVPGPSPNEENNGKSMSLKN", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "A", "comment": "Abolishes interaction with BCL6 and inhibits BCL6 corepression activity; when associated with A-507 and A-511.", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.526.526", "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": "Q6W2J9-1.511.511", "start_pos": 511, "end_pos": 511, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Structure of a BCOR corepressor peptide in complex with the BCL6 BTB domain dimer.", "journal": "Molecular cell", "date": "2008", "authors": "Ghetu AF, Corcoran CM, Cerchietti L, Bardwell VJ, Melnick A, Prive GG", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "GNGCAIYRSEIISTAPSSWV", "down_seq": "PGPSPNEENNGKSMSLKNKA", "mutagenesis": [ { "sequence_org": "V", "sequence_mut": "A", "comment": "Abolishes interaction with BCL6 and inhibits BCL6 corepression activity; when associated with A-507 and A-509.", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "18280243", "url": "https://glygen.org/publication/PubMed/18280243" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.531.531", "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": "Q6W2J9-1.1459.1459", "start_pos": 1459, "end_pos": 1459, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "SPQETTQSRPMPPEARRLIV", "down_seq": "KNAGETLLQRAARLGYEEVV", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "18", "frequency": "0.4", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 2 filters: patient count (18/4799); num. of cancers (9).", "chr_id": "23", "chr_pos": "40062191", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N1459", "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: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: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: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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.1441.1441", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.1461.1461", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.1463.1463", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1464.1464", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1043.1043", "start_pos": 1043, "end_pos": 1043, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "M", "start_aa": "M", "up_seq": "FSELEMKEREGGHPATKDSE", "down_seq": "CKFSPADWERLKGNQDKKPK", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "2053", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "M", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40071084", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "M1043", "disease": [ { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumour of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant urinary bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder malignant tumour", "description": "" }, { "id": "MIM:109800", "resource": "MIM", "url": "https://www.omim.org/entry/109800", "name": "Bladder cancer", "description": "Bladder cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "11054", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11054" } ] }, { "disease_id": "DOID: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.1045.1045", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1045.1045", "start_pos": 1045, "end_pos": 1045, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147174449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147174449", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147174449", "url": "https://www.ensembl.org/id/rs2147174449", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "ELEMKEREGGHPATKDSEMC", "down_seq": "FSPADWERLKGNQDKKPKSV", "snv": [ { "evidence": [ { "id": "rs2147174449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147174449" }, { "id": "rs2147174449", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147174449" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (KFS->NFS).", "chr_id": "X", "chr_pos": "40071076", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1045", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.1043.1043", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1076.1076", "start_pos": 1076, "end_pos": 1076, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "GNQDKKPKSVTLEEAIAEQN", "down_seq": "SERCEYSVGNKHRDPFEAPE", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40070985", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E1076", "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" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.1131.1131", "start_pos": 1131, "end_pos": 1131, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PVSEPPADQVASDMPHSPTL", "down_seq": "VDRKRKVSGDSSHTETTAEE", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40064447", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1131", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.1127.1127", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1136.1136", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.1139.1139", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.1141.1141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1136.1136", "start_pos": 1136, "end_pos": 1136, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PADQVASDMPHSPTLRVDRK", "down_seq": "KVSGDSSHTETTAEEVPEDP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40064431", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1136", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.1127.1127", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1131.1131", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.1139.1139", "categories": [ "phosphorylation_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1141.1141", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1141.1141", "start_pos": 1141, "end_pos": 1141, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1935087867", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935087867", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1935087867", "url": "https://www.ensembl.org/id/rs1935087867", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1935087867", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1935087867", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ASDMPHSPTLRVDRKRKVSG", "down_seq": "SSHTETTAEEVPEDPLLKAK", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1935087867", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935087867" }, { "id": "rs1935087867", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1935087867" }, { "id": "rs1935087867", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1935087867" } ], "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 (DSS->NSS).", "chr_id": "23", "chr_pos": "40064417", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1141", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.1127.1127", "categories": [ "phosphorylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.1131.1131", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1136.1136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.1139.1139", "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": "Q6W2J9-1.1163.1163", "start_pos": 1163, "end_pos": 1163, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SHTETTAEEVPEDPLLKAKR", "down_seq": "RVSKDDWPEREMTNSSSNHL", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40064351", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1163", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.1178.1178", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1178.1178", "start_pos": 1178, "end_pos": 1178, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs375639152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375639152", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs375639152", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs375639152", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs375639152", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375639152", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs375639152", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375639152#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs375639152", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375639152", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKAKRRRVSKDDWPEREMTN", "down_seq": "SSNHLEDPHYSELTNLKVCI", "snv": [ { "evidence": [ { "id": "rs375639152", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375639152" }, { "id": "rs375639152", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs375639152" }, { "id": "rs375639152", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs375639152" }, { "id": "rs375639152", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs375639152#frequency_tab" }, { "id": "rs375639152", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs375639152" } ], "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": "X", "chr_pos": "40063922", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1178", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.1163.1163", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.1195.1195", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1195.1195", "start_pos": 1195, "end_pos": 1195, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147061814", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147061814", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147061814", "url": "https://www.ensembl.org/id/rs2147061814", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MTNSSSNHLEDPHYSELTNL", "down_seq": "VCIELTGLHPKKQRHLLHLR", "snv": [ { "evidence": [ { "id": "rs2147061814", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147061814" }, { "id": "rs2147061814", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147061814" } ], "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": "X", "chr_pos": "40063871", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K1195", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.1178.1178", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.1209.1209", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1209.1209", "start_pos": 1209, "end_pos": 1209, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SELTNLKVCIELTGLHPKKQ", "down_seq": "HLLHLRERWEQQVSAADGKP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40063829", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R1209", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.1195.1195", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.1217.1217", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1217.1217", "start_pos": 1217, "end_pos": 1217, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "CIELTGLHPKKQRHLLHLRE", "down_seq": "WEQQVSAADGKPGRQSRKEV", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "40063806", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1217", "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: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" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.1209.1209", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1263.1263", "start_pos": 1263, "end_pos": 1263, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "PEAIPQGTNITEEKPGRKRA", "down_seq": "AKGNRSWSEESLKPSDNEQG", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "D", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40063666", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E1263", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.1269.1269", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1269.1269", "start_pos": 1269, "end_pos": 1269, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1157119031", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1157119031", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1157119031", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1157119031#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1157119031", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1157119031", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GTNITEEKPGRKRAEAKGNR", "down_seq": "WSEESLKPSDNEQGLPVFSG", "snv": [ { "evidence": [ { "id": "rs1157119031", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1157119031" }, { "id": "rs1157119031", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1157119031#frequency_tab" }, { "id": "rs1157119031", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1157119031" } ], "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 (SWS->NWS).", "chr_id": "X", "chr_pos": "40063649", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1269", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.1263.1263", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1295.1295", "start_pos": 1295, "end_pos": 1295, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1194416266", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194416266", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1194416266", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194416266#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1194416266", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194416266", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "LKPSDNEQGLPVFSGSPPMK", "down_seq": "LSSTSAGGKKQAQPSCAPAS", "snv": [ { "evidence": [ { "id": "rs1194416266", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1194416266" }, { "id": "rs1194416266", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1194416266#frequency_tab" }, { "id": "rs1194416266", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1194416266" } ], "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": "X", "chr_pos": "40063035", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S1295", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1290.1290", "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": "Q6W2J9-1.129.129", "start_pos": 129, "end_pos": 129, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1243995590", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243995590", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1243995590", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1243995590#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1243995590", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243995590", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1243995590", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1243995590", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "LGGLGFSSERNPEMQFKPNT", "down_seq": "ETVEASAVSGKPPNGFSAIY", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1243995590", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1243995590" }, { "id": "rs1243995590", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1243995590#frequency_tab" }, { "id": "rs1243995590", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1243995590" }, { "id": "rs1243995590", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1243995590" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NTP->NTS).", "chr_id": "23", "chr_pos": "40074961", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P129", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.145.145", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1352.1352", "start_pos": 1352, "end_pos": 1352, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs768842901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768842901", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs768842901", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768842901", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs768842901", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768842901#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs768842901", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768842901", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs768842901", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs768842901", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VLCADEEEDCQAASLLQKYT", "down_seq": "NSEKPSGKRLCKTKHLIPQE", "snv": [ { "evidence": [ { "id": "rs768842901", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768842901" }, { "id": "rs768842901", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs768842901" }, { "id": "rs768842901", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs768842901#frequency_tab" }, { "id": "rs768842901", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs768842901" }, { "id": "rs768842901", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs768842901" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (DNS->NNS).", "chr_id": "X", "chr_pos": "40062865", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1352", "keywords": [ "ebi", "somatic" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.1345.1345", "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": "Q6W2J9-1.1375.1375", "start_pos": 1375, "end_pos": 1375, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "EKPSGKRLCKTKHLIPQESR", "down_seq": "GLPLTGEYYVENADGKVTVR", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40062796", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1375", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.1391.1391", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.137.137", "start_pos": 137, "end_pos": 137, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ERNPEMQFKPNTPETVEASA", "down_seq": "SGKPPNGFSAIYKTPPGIQK", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "I", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "40074937", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V137", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID: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" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.152.152", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1391.1391", "start_pos": 1391, "end_pos": 1391, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QESRRGLPLTGEYYVENADG", "down_seq": "VTVRRFRKRPEPSSDYDLSP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "K", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (KVT->NVT).", "chr_id": "23", "chr_pos": "40062746", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1391", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.1375.1375", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.1405.1405", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.1408.1408", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.1410.1410", "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": "Q6W2J9-1.1405.1405", "start_pos": 1405, "end_pos": 1405, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VENADGKVTVRRFRKRPEPS", "down_seq": "DYDLSPAKQEPKPFDRLQQL", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "23", "chr_pos": "40062353", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S1405", "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" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.1391.1391", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.1408.1408", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1410.1410", "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": "Q6W2J9-1.1408.1408", "start_pos": 1408, "end_pos": 1408, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2147014539", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147014539", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147014539", "url": "https://www.ensembl.org/id/rs2147014539", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ADGKVTVRRFRKRPEPSSDY", "down_seq": "LSPAKQEPKPFDRLQQLLPA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs2147014539", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147014539" }, { "id": "rs2147014539", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147014539" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "55594", "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": "23", "chr_pos": "40062345", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1408", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.1391.1391", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.1405.1405", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.1410.1410", "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": "Q6W2J9-1.1430.1430", "start_pos": 1430, "end_pos": 1430, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "SPAKQEPKPFDRLQQLLPAS", "down_seq": "STQLPCSSSPQETTQSRPMP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40062279", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q1430", "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": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.1410.1410", "categories": [ "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.1441.1441", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1441.1441", "start_pos": 1441, "end_pos": 1441, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "RLQQLLPASQSTQLPCSSSP", "down_seq": "ETTQSRPMPPEARRLIVNKN", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40062246", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q1441", "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: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": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.1430.1430", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.1459.1459", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.1461.1461", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1444.1444", "start_pos": 1444, "end_pos": 1444, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1203501550", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203501550", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1203501550", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1203501550#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1203501550", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203501550", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "QLLPASQSTQLPCSSSPQET", "down_seq": "QSRPMPPEARRLIVNKNAGE", "snv": [ { "evidence": [ { "id": "rs1203501550", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1203501550" }, { "id": "rs1203501550", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1203501550#frequency_tab" }, { "id": "rs1203501550", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1203501550" } ], "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 (TQS->NQS).", "chr_id": "X", "chr_pos": "40062236", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T1444", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.1430.1430", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.1441.1441", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.1459.1459", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.1461.1461", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.1463.1463", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.1464.1464", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1445.1445", "start_pos": 1445, "end_pos": 1445, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "LLPASQSTQLPCSSSPQETT", "down_seq": "SRPMPPEARRLIVNKNAGET", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40062234", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q1445", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.1430.1430", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.1441.1441", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.1459.1459", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.1461.1461", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.1463.1463", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.1464.1464", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.145.145", "start_pos": 145, "end_pos": 145, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147271508", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147271508", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147271508", "url": "https://www.ensembl.org/id/rs2147271508", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "KPNTPETVEASAVSGKPPNG", "down_seq": "SAIYKTPPGIQKSAVATAEA", "snv": [ { "evidence": [ { "id": "rs2147271508", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147271508" }, { "id": "rs2147271508", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147271508" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGF->NGS).", "chr_id": "X", "chr_pos": "40074912", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F145", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.129.129", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1461.1461", "start_pos": 1461, "end_pos": 1461, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147000925", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147000925", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147000925", "url": "https://www.ensembl.org/id/rs2147000925", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "QETTQSRPMPPEARRLIVNK", "down_seq": "AGETLLQRAARLGYEEVVLY", "snv": [ { "evidence": [ { "id": "rs2147000925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147000925" }, { "id": "rs2147000925", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147000925" } ], "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": "X", "chr_pos": "40062185", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1461", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs2147000925", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147000925" }, { "id": "rs2147000925", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147000925" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NKN->NKT).", "chr_id": "X", "chr_pos": "40062185", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N1461", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.1441.1441", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.1459.1459", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.1463.1463", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.1464.1464", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "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": "Q6W2J9-1.1463.1463", "start_pos": 1463, "end_pos": 1463, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147000563", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147000563", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147000563", "url": "https://www.ensembl.org/id/rs2147000563", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2147000563", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2147000563", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "TTQSRPMPPEARRLIVNKNA", "down_seq": "ETLLQRAARLGYEEVVLYCL", "snv": [ { "evidence": [ { "id": "rs2147000563", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147000563" }, { "id": "rs2147000563", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147000563" }, { "id": "rs2147000563", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2147000563" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NAG->NAS).", "chr_id": "NC_000023.11", "chr_pos": "40062180", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G1463", "keywords": [ "ebi", "somatic", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.1459.1459", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.1461.1461", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.1464.1464", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1464.1464", "start_pos": 1464, "end_pos": 1464, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "TQSRPMPPEARRLIVNKNAG", "down_seq": "TLLQRAARLGYEEVVLYCLE", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "40062177", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E1464", "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: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: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.1444.1444", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.1445.1445", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1459.1459", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.1461.1461", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.1463.1463", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1486.1486", "start_pos": 1486, "end_pos": 1486, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs2146924590", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2146924590", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2146924590", "url": "https://www.ensembl.org/id/rs2146924590", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs2146924590", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2146924590", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "LLQRAARLGYEEVVLYCLEN", "down_seq": "ICDVNHRDNAGYCALHEACA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs2146924590", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2146924590" }, { "id": "rs2146924590", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2146924590" }, { "id": "rs2146924590", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs2146924590" } ], "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 (KIC->NIC).", "chr_id": "23", "chr_pos": "40057292", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "K1486", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.1514.1514", "start_pos": 1514, "end_pos": 1514, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "DNAGYCALHEACARGWLNIV", "down_seq": "HLLEYGADVNCSAQDGTRPL", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "0", "subjects_positive": "0", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (7).", "chr_id": "23", "chr_pos": "40057210", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1514", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.152.152", "start_pos": 152, "end_pos": 152, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "VEASAVSGKPPNGFSAIYKT", "down_seq": "PGIQKSAVATAEALGLDRPA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "5", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40074891", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P152", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.137.137", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.165.165", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1536.1536", "start_pos": 1536, "end_pos": 1536, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLEYGADVNCSAQDGTRPLH", "down_seq": "AVENDHLEIVRLLLSYGADP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40055503", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1536", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.1547.1547", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1547.1547", "start_pos": 1547, "end_pos": 1547, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "AQDGTRPLHDAVENDHLEIV", "down_seq": "LLLSYGADPTLATYSGRTIM", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "3", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40055470", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1547", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.1536.1536", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.1562.1562", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1562.1562", "start_pos": 1562, "end_pos": 1562, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HLEIVRLLLSYGADPTLATY", "down_seq": "GRTIMKMTHSELMEKFLTDY", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40055424", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S1562", "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": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.1547.1547", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1588.1588", "start_pos": 1588, "end_pos": 1588, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "KMTHSELMEKFLTDYLNDLQ", "down_seq": "RNDDDASGTWDFYGSSVCEP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40054313", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G1588", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1593.1593", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.1598.1598", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1593.1593", "start_pos": 1593, "end_pos": 1593, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2146871084", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2146871084", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2146871084", "url": "https://www.ensembl.org/id/rs2146871084", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "ELMEKFLTDYLNDLQGRNDD", "down_seq": "ASGTWDFYGSSVCEPDDESG", "snv": [ { "evidence": [ { "id": "rs2146871084", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2146871084" }, { "id": "rs2146871084", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2146871084" } ], "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": "X", "chr_pos": "40054298", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D1593", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1588.1588", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1598.1598", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.1611.1611", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1598.1598", "start_pos": 1598, "end_pos": 1598, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "FLTDYLNDLQGRNDDDASGT", "down_seq": "DFYGSSVCEPDDESGYDVLA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "W", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40054282", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "W1598", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.1588.1588", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1593.1593", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.1611.1611", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1611.1611", "start_pos": 1611, "end_pos": 1611, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DDDASGTWDFYGSSVCEPDD", "down_seq": "SGYDVLANPPGPEDQDDDDD", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40054031", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E1611", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.1593.1593", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.1598.1598", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.1627.1627", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_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": "Q6W2J9-1.1627.1627", "start_pos": 1627, "end_pos": 1627, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EPDDESGYDVLANPPGPEDQ", "down_seq": "DDDDAYSDVFEFEFSETPLL", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "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": "40053983", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D1627", "disease": [ { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.1611.1611", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.165.165", "start_pos": 165, "end_pos": 165, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "FSAIYKTPPGIQKSAVATAE", "down_seq": "LGLDRPASDKQSPLNINGAS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40074852", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A165", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.145.145", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.152.152", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1661.1661", "start_pos": 1661, "end_pos": 1661, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "FSETPLLPCYNIQVSVAQGP", "down_seq": "NWLLLSDVLKKLKMSSRIFR", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "2617", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40052396", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1661", "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" } ] }, { "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.1681.1681", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1681.1681", "start_pos": 1681, "end_pos": 1681, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RNWLLLSDVLKKLKMSSRIF", "down_seq": "CNFPNVEIVTIAEAEFYRQV", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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 (4).", "chr_id": "23", "chr_pos": "40052336", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R1681", "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:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.1661.1661", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.1691.1691", "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": "Q6W2J9-1.1732.1732", "start_pos": 1732, "end_pos": 1732, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "DLEAFNPESKELLDLVEFTN", "down_seq": "IQTLLGSSVEWLHPSDLASD", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "E", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40052183", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "E1732", "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" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.1733.1733", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1733.1733", "start_pos": 1733, "end_pos": 1733, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs373263562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373263562", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs373263562", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373263562", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs373263562", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373263562#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs373263562", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373263562", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "I", "start_aa": "I", "up_seq": "LEAFNPESKELLDLVEFTNE", "down_seq": "QTLLGSSVEWLHPSDLASDN", "snv": [ { "evidence": [ { "id": "rs373263562", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373263562" }, { "id": "rs373263562", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs373263562" }, { "id": "rs373263562", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs373263562#frequency_tab" }, { "id": "rs373263562", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs373263562" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "I", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (IQT->NQT).", "chr_id": "X", "chr_pos": "40052179", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "I1733", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.1732.1732", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1755.1755", "start_pos": 1755, "end_pos": 1755, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1485427754", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1485427754", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1485427754", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1485427754", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "TLLGSSVEWLHPSDLASDNY", "down_seq": "", "snv": [ { "evidence": [ { "id": "rs1485427754", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1485427754" }, { "id": "rs1485427754", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1485427754" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "W", "sequence_mut": "C", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NYW->NYC).", "chr_id": "X", "chr_pos": "40052112", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "W1755", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.182.182", "start_pos": 182, "end_pos": 182, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs148105564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148105564", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs148105564", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148105564", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs148105564", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148105564#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs148105564", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148105564", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs148105564", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs148105564", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "TAEALGLDRPASDKQSPLNI", "down_seq": "GASYLRLPWVNPYMEGATPA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs148105564", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148105564" }, { "id": "rs148105564", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs148105564" }, { "id": "rs148105564", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs148105564#frequency_tab" }, { "id": "rs148105564", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs148105564" }, { "id": "rs148105564", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs148105564" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "N", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NIN->NIS).", "chr_id": "23", "chr_pos": "40074801", "ref_nt": "T", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "N182", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.184.184", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.188.188", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.184.184", "start_pos": 184, "end_pos": 184, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs190780449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190780449", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs190780449", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190780449", "database": "1000Genomes", "categories": [ "Other" ] }, { "id": "rs190780449", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190780449", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs190780449", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190780449", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "EALGLDRPASDKQSPLNING", "down_seq": "SYLRLPWVNPYMEGATPAIY", "snv": [ { "evidence": [ { "id": "rs190780449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190780449" }, { "id": "rs190780449", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190780449" }, { "id": "rs190780449", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190780449" }, { "id": "rs190780449", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190780449" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "A", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NGA->NGS).", "chr_id": "X", "chr_pos": "40074796", "ref_nt": "A", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A184", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs190780449", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190780449" }, { "id": "rs190780449", "database": "1000Genomes", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs190780449" }, { "id": "rs190780449", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs190780449" }, { "id": "rs190780449", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs190780449" } ], "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": "X", "chr_pos": "40074796", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A184", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.165.165", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.188.188", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 2 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "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": "Q6W2J9-1.188.188", "start_pos": 188, "end_pos": 188, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "LDRPASDKQSPLNINGASYL", "down_seq": "LPWVNPYMEGATPAIYPFLD", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "W", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40074784", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R188", "disease": [ { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.182.182", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.184.184", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.218.218", "start_pos": 218, "end_pos": 218, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147265995", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147265995", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147265995", "url": "https://www.ensembl.org/id/rs2147265995", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "GATPAIYPFLDSPNKYSLNM", "down_seq": "KALLPQQSYSLAQPLYSPVC", "snv": [ { "evidence": [ { "id": "rs2147265995", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147265995" }, { "id": "rs2147265995", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147265995" } ], "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 (NMY->NMC).", "chr_id": "X", "chr_pos": "40074693", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y218", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.259.259", "start_pos": 259, "end_pos": 259, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TNGERFLYLPPPHYVGPHIP", "down_seq": "SLASPMRLSTPSASPAIPPL", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40074570", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S259", "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: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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.246.246", "categories": [ "glycosylation_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6W2J9-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.274.274", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.271.271", "start_pos": 271, "end_pos": 271, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147214767", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147214767", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147214767", "url": "https://www.ensembl.org/id/rs2147214767", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "HYVGPHIPSSLASPMRLSTP", "down_seq": "ASPAIPPLVHCADKSLPWKM", "snv": [ { "evidence": [ { "id": "rs2147214767", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147214767" }, { "id": "rs2147214767", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147214767" } ], "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": "X", "chr_pos": "40072947", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S271", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6W2J9-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.274.274", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.284.284", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.274.274", "start_pos": 274, "end_pos": 274, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "GPHIPSSLASPMRLSTPSAS", "down_seq": "AIPPLVHCADKSLPWKMGVS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "P", "sequence_mut": "A", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40074526", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "P274", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.259.259", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.284.284", "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": "Q6W2J9-1.27.27", "start_pos": 27, "end_pos": 27, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "LYGNVHSWMNSERVRMCGAS", "down_seq": "DRKILVNDGDASKARLELRE", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40077851", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E27", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.38.38", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.284.284", "start_pos": 284, "end_pos": 284, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs977644059", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs977644059", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs977644059", "url": "https://www.ncbi.nlm.nih.gov/snp/rs977644059#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs977644059", "url": "http://gnomad.broadinstitute.org/awesome?query=rs977644059", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "PMRLSTPSASPAIPPLVHCA", "down_seq": "KSLPWKMGVSPGNPVDSHAY", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs977644059", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs977644059" }, { "id": "rs977644059", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs977644059#frequency_tab" }, { "id": "rs977644059", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs977644059" } ], "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 (DKS->NKS).", "chr_id": "23", "chr_pos": "40074496", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D284", "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:0111809", "recommended_name": { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "syndromic microphthalmia 2", "description": "A syndromic microphthalmia characterized by ocular defects including microphthalmia, microcornea, and congentital cataract; facial dysmorphism including septate nasal cartilage with high nasal bridge; congenital heart defects, most commonly a septal defect; and dental anomalies, most commonly persistent primary teeth and radiculomegaly that has_material_basis_in mutation in the BCL6 corepressor gene on chromosome Xp11." }, "synonyms": [ { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "ANOP2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "MAA2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "MCOPS2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "OFCD syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "oculofaciocardiodental syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "syndromic microphthalmia type 2", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "cataract-microphthalmia-radiculomegaly-cardiac septal defect syndrome", "description": "" }, { "id": "DOID:0111809", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:0111809", "name": "microphthalmia cataracts radiculomegaly and septal heart defects", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "OFCD syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "cataract-microphthalmia-radiculomegaly-cardiac septal defect syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic 2, X-linked dominant", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia, syndromic type 2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "oculofaciocardiodental syndrome", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "ANOP2 (formerly)", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "MAA2 (formerly)", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "MCOPS2", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "microphthalmia cataracts radiculomegaly and septal heart defects", "description": "" }, { "id": "MONDO:0010261", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010261", "name": "syndromic microphthalmia type 2", "description": "" }, { "id": "MIM:300166", "resource": "MIM", "url": "https://www.omim.org/entry/300166", "name": "Microphthalmia, syndromic, 2", "description": "Microphthalmia, syndromic, 2" } ], "unlinked_id_list": [], "evidence": [ { "id": "300166", "database": "MIM", "url": "https://www.omim.org/entry/300166" }, { "id": "0111809", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:0111809" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease", "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.271.271", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.274.274", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.311.311", "start_pos": 311, "end_pos": 311, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147258066", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147258066", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147258066", "url": "https://www.ensembl.org/id/rs2147258066", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "MGVSPGNPVDSHAYPHIQNS", "down_seq": "QPRVPSAKAVTSGLPGDTAL", "snv": [ { "evidence": [ { "id": "rs2147258066", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147258066" }, { "id": "rs2147258066", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147258066" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "K", "sequence_mut": "T", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NSK->NST).", "chr_id": "X", "chr_pos": "40074414", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "K311", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.320.320", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.320.320", "start_pos": 320, "end_pos": 320, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "DSHAYPHIQNSKQPRVPSAK", "down_seq": "VTSGLPGDTALLLPPSPRPS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40074387", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A320", "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: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.311.311", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.340.340", "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": "Q6W2J9-1.342.342", "start_pos": 342, "end_pos": 342, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "TSGLPGDTALLLPPSPRPSP", "down_seq": "VHLPTQPAADTYSEFHKHYA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40074322", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R342", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.340.340", "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": "Q6W2J9-1.35.35", "start_pos": 35, "end_pos": 35, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "MNSERVRMCGASEDRKILVN", "down_seq": "GDASKARLELREENPLNHNV", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "Y", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40076516", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "D35", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.54.54", "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": "Q6W2J9-1.38.38", "start_pos": 38, "end_pos": 38, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "ERVRMCGASEDRKILVNDGD", "down_seq": "SKARLELREENPLNHNVVDA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40076507", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A38", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.27.27", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.54.54", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.57.57", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.3.3", "start_pos": 3, "end_pos": 3, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ML", "down_seq": "ATPLYGNVHSWMNSERVRMC", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "320", "subjects_positive": "1", "frequency": "0.3", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40077922", "ref_nt": "G", "alt_nt": "C", "minor_allelic_frequency": "", "site_lbl": "S3", "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:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "3", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40077922", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S3", "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: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.404.404", "start_pos": 404, "end_pos": 404, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "PAARLSNGKYPKAPEGGEGA", "down_seq": "PVPGHARKTAVQDRKDGSSP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "H", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40074134", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q404", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.423.423", "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": "Q6W2J9-1.420.420", "start_pos": 420, "end_pos": 420, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1935641686", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935641686", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1935641686", "url": "https://www.ensembl.org/id/rs1935641686", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "GEGAQPVPGHARKTAVQDRK", "down_seq": "GSSPPLLEKQTVTKDVTDKP", "snv": [ { "evidence": [ { "id": "rs1935641686", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935641686" }, { "id": "rs1935641686", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1935641686" } ], "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": "X", "chr_pos": "40074088", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D420", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.423.423", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.431.431", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.435.435", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.423.423", "start_pos": 423, "end_pos": 423, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "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": "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": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AQPVPGHARKTAVQDRKDGS", "down_seq": "PPLLEKQTVTKDVTDKPLDL", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40074078", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S423", "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" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "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": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser423" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag", "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.404.404", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.431.431", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6W2J9-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.442.442", "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": 4 } ], "sort_fields": [ "title", "journal", "date", "authors" ] } ] }, { "id": "Q6W2J9-1.431.431", "start_pos": 431, "end_pos": 431, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1239618544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1239618544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1239618544", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1239618544", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "RKTAVQDRKDGSSPPLLEKQ", "down_seq": "VTKDVTDKPLDLSSKVVDVD", "snv": [ { "evidence": [ { "id": "rs1239618544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1239618544" }, { "id": "rs1239618544", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1239618544" } ], "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 (TVT->NVT).", "chr_id": "X", "chr_pos": "40074054", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T431", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.423.423", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.442.442", "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": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.435.435", "start_pos": 435, "end_pos": 435, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147246150", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147246150", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147246150", "url": "https://www.ensembl.org/id/rs2147246150", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "VQDRKDGSSPPLLEKQTVTK", "down_seq": "VTDKPLDLSSKVVDVDASKA", "snv": [ { "evidence": [ { "id": "rs2147246150", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147246150" }, { "id": "rs2147246150", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147246150" } ], "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": "X", "chr_pos": "40074043", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D435", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.420.420", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6W2J9-1.423.423", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.431.431", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.442.442", "categories": [ "snv_flag" ] }, { "distance": 18, "direction": "upstream", "id": "Q6W2J9-1.453.453", "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": "Q6W2J9-1.442.442", "start_pos": 442, "end_pos": 442, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "SSPPLLEKQTVTKDVTDKPL", "down_seq": "LSSKVVDVDASKADHMKKMA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "2617", "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": "23", "chr_pos": "40074022", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D442", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.423.423", "categories": [ "snv_flag", "phosphorylation_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.431.431", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.435.435", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.453.453", "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": "Q6W2J9-1.483.483", "start_pos": 483, "end_pos": 483, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PTVLVHSRAGSGLVLSGSEI", "down_seq": "KETLSPPGNGCAIYRSEIIS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (4).", "chr_id": "23", "chr_pos": "40073898", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P483", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.518.518", "start_pos": 518, "end_pos": 518, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "RSEIISTAPSSWVVPGPSPN", "down_seq": "ENNGKSMSLKNKALDWAIPQ", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "E", "sequence_mut": "K", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073794", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E518", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.531.531", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.522.522", "start_pos": 522, "end_pos": 522, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "ISTAPSSWVVPGPSPNEENN", "down_seq": "KSMSLKNKALDWAIPQQRSS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (NNG->NNS).", "chr_id": "23", "chr_pos": "40073782", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G522", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.531.531", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.524.524", "start_pos": 524, "end_pos": 524, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147240300", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147240300", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147240300", "url": "https://www.ensembl.org/id/rs2147240300", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TAPSSWVVPGPSPNEENNGK", "down_seq": "MSLKNKALDWAIPQQRSSSC", "snv": [ { "evidence": [ { "id": "rs2147240300", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147240300" }, { "id": "rs2147240300", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147240300" } ], "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 (SMS->NMS).", "chr_id": "X", "chr_pos": "40073775", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S524", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.531.531", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.526.526", "start_pos": 526, "end_pos": 526, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSSWVVPGPSPNEENNGKSM", "down_seq": "LKNKALDWAIPQQRSSSCPR", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40073769", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "S526", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.507.507", "categories": [ "mutagenesis_flag" ] }, { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.508.508", "categories": [ "mutagenesis_flag" ] }, { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.509.509", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.531.531", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.546.546", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.531.531", "start_pos": 531, "end_pos": 531, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs749142863", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749142863", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs749142863", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749142863", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs749142863", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749142863", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "VPGPSPNEENNGKSMSLKNK", "down_seq": "LDWAIPQQRSSSCPRMGGTD", "snv": [ { "evidence": [ { "id": "rs749142863", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749142863" }, { "id": "rs749142863", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs749142863" }, { "id": "rs749142863", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs749142863" } ], "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": "X", "chr_pos": "40073755", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "A531", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.511.511", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.546.546", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.535.535", "start_pos": 535, "end_pos": 535, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "SPNEENNGKSMSLKNKALDW", "down_seq": "IPQQRSSSCPRMGGTDAVIT", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1773", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073742", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "A535", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.518.518", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.522.522", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.524.524", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.531.531", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.546.546", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.555.555", "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": "Q6W2J9-1.546.546", "start_pos": 546, "end_pos": 546, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SLKNKALDWAIPQQRSSSCP", "down_seq": "MGGTDAVITNVSGSVSSAGR", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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 (5).", "chr_id": "23", "chr_pos": "40073709", "ref_nt": "C", "alt_nt": "T", "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:263", "recommended_name": { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "kidney cancer", "description": "A urinary system cancer that is located_in the kidney." }, "synonyms": [ { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant neoplasm of kidney except pelvis", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "malignant tumour of kidney", "description": "" }, { "id": "DOID:263", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:263", "name": "renal cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3675", "DOID:4455" ], "evidence": [ { "id": "263", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:263" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.526.526", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.531.531", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.535.535", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.555.555", "categories": [ "glycosylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.560.560", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.563.563", "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": "Q6W2J9-1.54.54", "start_pos": 54, "end_pos": 54, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1435258487", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435258487", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1435258487", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1435258487#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1435258487", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435258487", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "N", "start_aa": "N", "up_seq": "NDGDASKARLELREENPLNH", "down_seq": "VVDASTAHRIDGLAALSMDR", "snv": [ { "evidence": [ { "id": "rs1435258487", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1435258487" }, { "id": "rs1435258487", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1435258487#frequency_tab" }, { "id": "rs1435258487", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1435258487" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "N", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NHN->NHS).", "chr_id": "X", "chr_pos": "40076458", "ref_nt": "C", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "N54", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.35.35", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "upstream", "id": "Q6W2J9-1.57.57", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.570.570", "start_pos": 570, "end_pos": 570, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "TDAVITNVSGSVSSAGRPAS", "down_seq": "SPAPNANADGTKTSRSSVET", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073638", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A570", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.555.555", "categories": [ "glycosylation_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.560.560", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.563.563", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.581.581", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.586.586", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.587.587", "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": "Q6W2J9-1.57.57", "start_pos": 57, "end_pos": 57, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147284544", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147284544", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147284544", "url": "https://www.ensembl.org/id/rs2147284544", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "DASKARLELREENPLNHNVV", "down_seq": "ASTAHRIDGLAALSMDRTGL", "snv": [ { "evidence": [ { "id": "rs2147284544", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147284544" }, { "id": "rs2147284544", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147284544" } ], "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": "X", "chr_pos": "40075177", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D57", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.38.38", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.54.54", "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": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.581.581", "start_pos": 581, "end_pos": 581, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VSSAGRPASASPAPNANADG", "down_seq": "KTSRSSVETTPSVIQHVGQP", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TKT->NKT).", "chr_id": "23", "chr_pos": "40073604", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T581", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "Q6W2J9-1.563.563", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.570.570", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.586.586", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.587.587", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.596.596", "start_pos": 596, "end_pos": 596, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "Q", "start_aa": "Q", "up_seq": "ANADGTKTSRSSVETTPSVI", "down_seq": "HVGQPPATPAKHSSSTSSKG", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "Q", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073560", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "Q596", "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" } ] }, { "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.581.581", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.586.586", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 9, "direction": "downstream", "id": "Q6W2J9-1.587.587", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.609.609", "categories": [ "snv_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.611.611", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.598.598", "start_pos": 598, "end_pos": 598, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "ADGTKTSRSSVETTPSVIQH", "down_seq": "GQPPATPAKHSSSTSSKGAK", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "4484", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073554", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V598", "disease": [ { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial breast carcinoma", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "familial cancer of the breast", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.581.581", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6W2J9-1.586.586", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.587.587", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 11, "direction": "upstream", "id": "Q6W2J9-1.609.609", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6W2J9-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "upstream", "id": "Q6W2J9-1.611.611", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.609.609", "start_pos": 609, "end_pos": 609, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs748027304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748027304", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs748027304", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748027304", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs748027304", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748027304#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs748027304", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748027304", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ETTPSVIQHVGQPPATPAKH", "down_seq": "SSTSSKGAKASNPEPSFKAN", "snv": [ { "evidence": [ { "id": "rs748027304", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748027304" }, { "id": "rs748027304", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs748027304" }, { "id": "rs748027304", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs748027304#frequency_tab" }, { "id": "rs748027304", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs748027304" } ], "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": "X", "chr_pos": "40073520", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S609", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.611.611", "categories": [ "snv_flag" ] }, { "distance": 8, "direction": "upstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.610.610", "start_pos": 610, "end_pos": 610, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs776440343", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776440343", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs776440343", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776440343", "database": "ExAC", "categories": [ "Other" ] }, { "id": "rs776440343", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776440343", "database": "gnomAD", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TTPSVIQHVGQPPATPAKHS", "down_seq": "STSSKGAKASNPEPSFKANE", "snv": [ { "evidence": [ { "id": "rs776440343", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776440343" }, { "id": "rs776440343", "database": "ExAC", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs776440343" }, { "id": "rs776440343", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs776440343" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SST->NST).", "chr_id": "X", "chr_pos": "40073517", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S610", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 14, "direction": "downstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "downstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.609.609", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "upstream", "id": "Q6W2J9-1.611.611", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.611.611", "start_pos": 611, "end_pos": 611, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] }, { "id": "rs1935595804", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935595804", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1935595804", "url": "https://www.ensembl.org/id/rs1935595804", "database": "ENSEMBL", "categories": [ "Other" ] }, { "id": "rs1935595804", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1935595804", "database": "COSMIC", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "TPSVIQHVGQPPATPAKHSS", "down_seq": "TSSKGAKASNPEPSFKANEN", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" }, { "id": "rs1935595804", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935595804" }, { "id": "rs1935595804", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1935595804" }, { "id": "rs1935595804", "database": "COSMIC", "url": "https://www.ensembl.org/homo_sapiens/Variation/Explore?v=rs1935595804" } ], "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 (STS->NTS).", "chr_id": "23", "chr_pos": "40073514", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S611", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.596.596", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.609.609", "categories": [ "snv_flag" ] }, { "distance": 1, "direction": "downstream", "id": "Q6W2J9-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.617.617", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.617.617", "start_pos": 617, "end_pos": 617, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "A", "start_aa": "A", "up_seq": "HVGQPPATPAKHSSSTSSKG", "down_seq": "KASNPEPSFKANENGLPPSS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "3601", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "T", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073497", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A617", "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": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.598.598", "categories": [ "snv_flag" ] }, { "distance": 13, "direction": "downstream", "id": "Q6W2J9-1.604.604", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.609.609", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.610.610", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.611.611", "categories": [ "snv_flag" ] }, { "distance": 19, "direction": "upstream", "id": "Q6W2J9-1.636.636", "categories": [ "glycosylation_flag", "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.637.637", "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": "Q6W2J9-1.677.677", "start_pos": 677, "end_pos": 677, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "YLPYPAPEGIAVSPLSLHGK", "down_seq": "PVYPHPVLLPNGSLFPGHLA", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "2", "frequency": "0.1", "sequence_org": "G", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073317", "ref_nt": "C", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "G677", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.709.709", "start_pos": 709, "end_pos": 709, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "G", "start_aa": "G", "up_seq": "GSLFPGHLAPKPGLPYGLPT", "down_seq": "RPEFVTYQDALGLGMVHPML", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "G", "sequence_mut": "S", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40073221", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "G709", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.764.764", "start_pos": 764, "end_pos": 764, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147220789", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147220789", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147220789", "url": "https://www.ensembl.org/id/rs2147220789", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "F", "start_aa": "F", "up_seq": "ERRSRSHERARYEDPTLRNR", "down_seq": "SEILETSSTKLHPDVPTDKN", "snv": [ { "evidence": [ { "id": "rs2147220789", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147220789" }, { "id": "rs2147220789", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147220789" } ], "glycoeffect": [ "n-glyco-sequon-gain" ], "sequence_org": "F", "sequence_mut": "S", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (NRF->NRS).", "chr_id": "X", "chr_pos": "40073055", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "F764", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.771.771", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.771.771", "start_pos": 771, "end_pos": 771, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1225745694", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225745694", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1225745694", "url": "https://www.ensembl.org/id/rs1225745694", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "ERARYEDPTLRNRFSEILET", "down_seq": "STKLHPDVPTDKNLKPNPNW", "snv": [ { "evidence": [ { "id": "rs1225745694", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1225745694" }, { "id": "rs1225745694", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1225745694" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "S", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (SST->NST).", "chr_id": "X", "chr_pos": "40073034", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "S771", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.764.764", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.810.810", "start_pos": 810, "end_pos": 810, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "NWNQGKTVVKSDKLVYVDLL", "down_seq": "EEPDAKTDTNVSKPSFAAES", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "720", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "R", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "40072918", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R810", "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: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.817.817", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.817.817", "start_pos": 817, "end_pos": 817, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147211947", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147211947", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147211947", "url": "https://www.ensembl.org/id/rs2147211947", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "VVKSDKLVYVDLLREEPDAK", "down_seq": "DTNVSKPSFAAESVGQSAEP", "snv": [ { "evidence": [ { "id": "rs2147211947", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147211947" }, { "id": "rs2147211947", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147211947" } ], "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 (TDT->NDT).", "chr_id": "X", "chr_pos": "40072896", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T817", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "Q6W2J9-1.810.810", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.844.844", "start_pos": 844, "end_pos": 844, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "P", "start_aa": "P", "up_seq": "PSFAAESVGQSAEPPKPSVE", "down_seq": "ALQQHRDFIALREELGRISD", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "P", "sequence_mut": "L", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "23", "chr_pos": "40072815", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "P844", "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: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:3571", "recommended_name": { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "liver cancer", "description": "A hepatobiliary system cancer that is located_in the liver." }, "synonyms": [ { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Ca liver - primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "Resectable malignant neoplasm of Liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "hepatic neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant hepato-biliary neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, primary", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant tumor of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "non-resectable primary hepatic malignant neoplasm", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary liver cancer", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "primary malignant neoplasm of liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "resectable malignant neoplasm of the liver", "description": "" }, { "id": "DOID:3571", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:3571", "name": "malignant neoplasm of liver, not specified as primary or secondary", "description": "" } ], "unlinked_id_list": [], "evidence": [ { "id": "3571", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:3571" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of upper third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of proximal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the middle third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "upstream", "id": "Q6W2J9-1.861.861", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.861.861", "start_pos": 861, "end_pos": 861, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "SVEPALQQHRDFIALREELG", "down_seq": "ISDFHETYTFKQPVFTVSKD", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [], "subjects_tested": "55594", "subjects_positive": "2", "frequency": "0.0", "sequence_org": "R", "sequence_mut": "C", "comment": "Somatic mutation passed 1 filters: num. of cancers (6).", "chr_id": "23", "chr_pos": "40072765", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R861", "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: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "Q6W2J9-1.844.844", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.867.867", "categories": [ "snv_flag" ] }, { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.877.877", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.867.867", "start_pos": 867, "end_pos": 867, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "E", "start_aa": "E", "up_seq": "QQHRDFIALREELGRISDFH", "down_seq": "TYTFKQPVFTVSKDSVLAGT", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40072747", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "E867", "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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 6, "direction": "downstream", "id": "Q6W2J9-1.861.861", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "upstream", "id": "Q6W2J9-1.877.877", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.877.877", "start_pos": 877, "end_pos": 877, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "EELGRISDFHETYTFKQPVF", "down_seq": "VSKDSVLAGTNKENLGLPVS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "T", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: n-glyco-sequon-gain (TVS->NVS).", "chr_id": "23", "chr_pos": "40072716", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "T877", "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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.861.861", "categories": [ "snv_flag" ] }, { "distance": 10, "direction": "downstream", "id": "Q6W2J9-1.867.867", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.908.908", "start_pos": 908, "end_pos": 908, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "NKENLGLPVSTPFLEPPLGS", "down_seq": "GPAVTFGKTQEDPKPFCVGS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "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": "23", "chr_pos": "40072624", "ref_nt": "C", "alt_nt": "G", "minor_allelic_frequency": "", "site_lbl": "D908", "keywords": [ "biomuta", "somatic", "cancer" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "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": "Q6W2J9-1.90.90", "start_pos": 90, "end_pos": 90, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs2147278138", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147278138", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs2147278138", "url": "https://www.ensembl.org/id/rs2147278138", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "LSMDRTGLIREGLRVPGNIV", "down_seq": "SSLCGLGSEKGREAATSTLG", "snv": [ { "evidence": [ { "id": "rs2147278138", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs2147278138" }, { "id": "rs2147278138", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs2147278138" } ], "glycoeffect": [ "n-glyco-sequon-gain", "o-glyco-site-loss" ], "sequence_org": "Y", "sequence_mut": "N", "comment": "Germline mutation passed 1 filters: n-glyco-sequon-gain (YSS->NSS).", "chr_id": "X", "chr_pos": "40075078", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "Y90", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "Q6W2J9-1.106.106", "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": "Q6W2J9-1.934.934", "start_pos": 934, "end_pos": 934, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "rs1935527239", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935527239", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1935527239", "url": "https://www.ensembl.org/id/rs1935527239", "database": "ENSEMBL", "categories": [ "Other" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "FGKTQEDPKPFCVGSAPPSV", "down_seq": "VTPTYTKDGADEAESNDGKV", "snv": [ { "evidence": [ { "id": "rs1935527239", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1935527239" }, { "id": "rs1935527239", "database": "ENSEMBL", "url": "https://www.ensembl.org/id/rs1935527239" } ], "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": "X", "chr_pos": "40072546", "ref_nt": "T", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "D934", "keywords": [ "ebi", "germline" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "upstream", "id": "Q6W2J9-1.949.949", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.949.949", "start_pos": 949, "end_pos": 949, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "APPSVDVTPTYTKDGADEAE", "down_seq": "NDGKVLKPKPSKLAKRIANS", "snv": [ { "evidence": [ { "id": "Q6W2J9", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q6W2J9" } ], "glycoeffect": [ "o-glyco-site-loss" ], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "S", "sequence_mut": "*", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "23", "chr_pos": "40072500", "ref_nt": "G", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "S949", "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: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: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": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 15, "direction": "downstream", "id": "Q6W2J9-1.934.934", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "Q6W2J9-1.1127.1127", "start_pos": 1127, "end_pos": 1127, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "VERQPVSEPPADQVASDMPH", "down_seq": "PTLRVDRKRKVSGDSSHTET", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "site_lbl": "Ser1127" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.1131.1131", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "Q6W2J9-1.1136.1136", "categories": [ "snv_flag" ] }, { "distance": 12, "direction": "upstream", "id": "Q6W2J9-1.1139.1139", "categories": [ "phosphorylation_flag" ] }, { "distance": 14, "direction": "upstream", "id": "Q6W2J9-1.1141.1141", "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": "Q6W2J9-1.1139.1139", "start_pos": 1139, "end_pos": 1139, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "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": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "QVASDMPHSPTLRVDRKRKV", "down_seq": "GDSSHTETTAEEVPEDPLLK", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "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": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser1139" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 12, "direction": "downstream", "id": "Q6W2J9-1.1127.1127", "categories": [ "phosphorylation_flag" ] }, { "distance": 8, "direction": "downstream", "id": "Q6W2J9-1.1131.1131", "categories": [ "snv_flag" ] }, { "distance": 3, "direction": "downstream", "id": "Q6W2J9-1.1136.1136", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.1141.1141", "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": "Q6W2J9-1.1290.1290", "start_pos": 1290, "end_pos": 1290, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "WSEESLKPSDNEQGLPVFSG", "down_seq": "PPMKSLSSTSAGGKKQAQPS", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser1290" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 5, "direction": "upstream", "id": "Q6W2J9-1.1295.1295", "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": "Q6W2J9-1.1345.1345", "start_pos": 1345, "end_pos": 1345, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "KENQKTDVLCADEEEDCQAA", "down_seq": "LLQKYTDNSEKPSGKRLCKT", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "site_lbl": "Ser1345" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "Q6W2J9-1.1352.1352", "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": "Q6W2J9-1.1410.1410", "start_pos": 1410, "end_pos": 1410, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "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": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "GKVTVRRFRKRPEPSSDYDL", "down_seq": "PAKQEPKPFDRLQQLLPASQ", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "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": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser1410" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 19, "direction": "downstream", "id": "Q6W2J9-1.1391.1391", "categories": [ "snv_flag" ] }, { "distance": 5, "direction": "downstream", "id": "Q6W2J9-1.1405.1405", "categories": [ "snv_flag" ] }, { "distance": 2, "direction": "downstream", "id": "Q6W2J9-1.1408.1408", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "Q6W2J9-1.1430.1430", "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": "Q6W2J9-1.336.336", "start_pos": 336, "end_pos": 336, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "PSAKAVTSGLPGDTALLLPP", "down_seq": "PRPSPRVHLPTQPAADTYSE", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser336" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "downstream", "id": "Q6W2J9-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "Q6W2J9-1.340.340", "categories": [ "phosphorylation_flag" ] }, { "distance": 6, "direction": "upstream", "id": "Q6W2J9-1.342.342", "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": "Q6W2J9-1.340.340", "start_pos": 340, "end_pos": 340, "uniprot_canonical_ac": "Q6W2J9-1", "length": 1755, "uniprot_id": "BCOR_HUMAN", "protein_name": "BCL-6 corepressor", "refseq_ac": "NP_001116855", "refseq_name": "BCL-6 corepressor isoform a", "gene_name": "BCOR", "gene_names_uniprotkb": "BCOR; KIAA1575", "gene_names_refseq": "ANOP2; BCOR; MAA2; MCOPS2", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" } ], "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": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "S", "start_aa": "S", "up_seq": "AVTSGLPGDTALLLPPSPRP", "down_seq": "PRVHLPTQPAADTYSEFHKH", "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Ser", "comment": "Phosphoserine", "evidence": [ { "database": "UniProtKB", "id": "Q6W2J9", "url": "https://www.uniprot.org/uniprotkb/Q6W2J9" }, { "database": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" }, { "database": "iPTMnet", "id": "Q6W2J9", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q6W2J9" } ], "site_lbl": "Ser340" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "453", "end_pos": "453" }, { "start_pos": "555", "end_pos": "555" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "1706", "end_pos": "1706" }, { "start_pos": "507", "end_pos": "507" }, { "start_pos": "508", "end_pos": "508" }, { "start_pos": "509", "end_pos": "509" }, { "start_pos": "511", "end_pos": "511" } ] }, { "type": "snv", "site_list": [ { "start_pos": "1459", "end_pos": "1459" }, { "start_pos": "1043", "end_pos": "1043" }, { "start_pos": "1045", "end_pos": "1045" }, { "start_pos": "106", "end_pos": "106" }, { "start_pos": "1076", "end_pos": "1076" }, { "start_pos": "1131", "end_pos": "1131" }, { "start_pos": "1136", "end_pos": "1136" }, { "start_pos": "1141", "end_pos": "1141" }, { "start_pos": "1163", "end_pos": "1163" }, { "start_pos": "1178", "end_pos": "1178" }, { "start_pos": "1195", "end_pos": "1195" }, { "start_pos": "1209", "end_pos": "1209" }, { "start_pos": "1217", "end_pos": "1217" }, { "start_pos": "1263", "end_pos": "1263" }, { "start_pos": "1269", "end_pos": "1269" }, { "start_pos": "1295", "end_pos": "1295" }, { "start_pos": "129", "end_pos": "129" }, { "start_pos": "1352", "end_pos": "1352" }, { "start_pos": "1375", "end_pos": "1375" }, { "start_pos": "137", "end_pos": "137" }, { "start_pos": "1391", "end_pos": "1391" }, { "start_pos": "1405", "end_pos": "1405" }, { "start_pos": "1408", "end_pos": "1408" }, { "start_pos": "1430", "end_pos": "1430" }, { "start_pos": "1441", "end_pos": "1441" }, { "start_pos": "1444", "end_pos": "1444" }, { "start_pos": "1445", "end_pos": "1445" }, { "start_pos": "145", "end_pos": "145" }, { "start_pos": "1461", "end_pos": "1461" }, { "start_pos": "1463", "end_pos": "1463" }, { "start_pos": "1464", "end_pos": "1464" }, { "start_pos": "1486", "end_pos": "1486" }, { "start_pos": "1514", "end_pos": "1514" }, { "start_pos": "152", "end_pos": "152" }, { "start_pos": "1536", "end_pos": "1536" }, { "start_pos": "1547", "end_pos": "1547" }, { "start_pos": "1562", "end_pos": "1562" }, { "start_pos": "1588", "end_pos": "1588" }, { "start_pos": "1593", "end_pos": "1593" }, { "start_pos": "1598", "end_pos": "1598" }, { "start_pos": "1611", "end_pos": "1611" }, { "start_pos": "1627", "end_pos": "1627" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "1661", "end_pos": "1661" }, { "start_pos": "1681", "end_pos": "1681" }, { "start_pos": "1691", "end_pos": "1691" }, { "start_pos": "1732", "end_pos": "1732" }, { "start_pos": "1733", "end_pos": "1733" }, { "start_pos": "1755", "end_pos": "1755" }, { "start_pos": "182", "end_pos": "182" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "188", "end_pos": "188" }, { "start_pos": "218", "end_pos": "218" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "271", "end_pos": "271" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "27", "end_pos": "27" }, { "start_pos": "284", "end_pos": "284" }, { "start_pos": "311", "end_pos": "311" }, { "start_pos": "320", "end_pos": "320" }, { "start_pos": "342", "end_pos": "342" }, { "start_pos": "35", "end_pos": "35" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "366", "end_pos": "366" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "369", "end_pos": "369" }, { "start_pos": "373", "end_pos": "373" }, { "start_pos": "378", "end_pos": "378" }, { "start_pos": "38", "end_pos": "38" }, { "start_pos": "3", "end_pos": "3" }, { "start_pos": "404", "end_pos": "404" }, { "start_pos": "420", "end_pos": "420" }, { "start_pos": "423", "end_pos": "423" }, { "start_pos": "431", "end_pos": "431" }, { "start_pos": "435", "end_pos": "435" }, { "start_pos": "442", "end_pos": "442" }, { "start_pos": "483", "end_pos": "483" }, { "start_pos": "518", "end_pos": "518" }, { "start_pos": "522", "end_pos": "522" }, { "start_pos": "524", "end_pos": "524" }, { "start_pos": "526", "end_pos": "526" }, { "start_pos": "531", "end_pos": "531" }, { "start_pos": "535", "end_pos": "535" }, { "start_pos": "546", "end_pos": "546" }, { "start_pos": "54", "end_pos": "54" }, { "start_pos": "560", "end_pos": "560" }, { "start_pos": "563", "end_pos": "563" }, { "start_pos": "570", "end_pos": "570" }, { "start_pos": "57", "end_pos": "57" }, { "start_pos": "581", "end_pos": "581" }, { "start_pos": "586", "end_pos": "586" }, { "start_pos": "587", "end_pos": "587" }, { "start_pos": "596", "end_pos": "596" }, { "start_pos": "598", "end_pos": "598" }, { "start_pos": "604", "end_pos": "604" }, { "start_pos": "609", "end_pos": "609" }, { "start_pos": "610", "end_pos": "610" }, { "start_pos": "611", "end_pos": "611" }, { "start_pos": "617", "end_pos": "617" }, { "start_pos": "636", "end_pos": "636" }, { "start_pos": "637", "end_pos": "637" }, { "start_pos": "677", "end_pos": "677" }, { "start_pos": "709", "end_pos": "709" }, { "start_pos": "764", "end_pos": "764" }, { "start_pos": "771", "end_pos": "771" }, { "start_pos": "810", "end_pos": "810" }, { "start_pos": "817", "end_pos": "817" }, { "start_pos": "844", "end_pos": "844" }, { "start_pos": "861", "end_pos": "861" }, { "start_pos": "867", "end_pos": "867" }, { "start_pos": "877", "end_pos": "877" }, { "start_pos": "908", "end_pos": "908" }, { "start_pos": "90", "end_pos": "90" }, { "start_pos": "934", "end_pos": "934" }, { "start_pos": "949", "end_pos": "949" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "1127", "end_pos": "1127" }, { "start_pos": "1139", "end_pos": "1139" }, { "start_pos": "1290", "end_pos": "1290" }, { "start_pos": "1345", "end_pos": "1345" }, { "start_pos": "1410", "end_pos": "1410" }, { "start_pos": "336", "end_pos": "336" }, { "start_pos": "340", "end_pos": "340" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "367", "end_pos": "367" }, { "start_pos": "423", "end_pos": "423" } ] } ], "categories": [ "phosphorylation_flag" ], "glycosylation": [], "mutagenesis": [], "snv": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "Q6W2J9-1.320.320", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "Q6W2J9-1.336.336", "categories": [ "phosphorylation_flag" ] }, { "distance": 2, "direction": "upstream", "id": "Q6W2J9-1.342.342", "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": "P42772-1.110.110", "start_pos": 110, "end_pos": 110, "uniprot_canonical_ac": "P42772-1", "length": 138, "uniprot_id": "CDN2B_HUMAN", "protein_name": "Cyclin-dependent kinase 4 inhibitor B", "refseq_ac": "NP_004927", "refseq_name": "cyclin-dependent kinase 4 inhibitor B isoform 1", "gene_name": "CDKN2B", "gene_names_uniprotkb": "CDKN2B; MTS2", "gene_names_refseq": "CDK4I; CDKN2B; INK4B; MTS2; P15; TP15; p15INK4b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42772", "url": "https://www.uniprot.org/uniprotkb/P42772" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42772", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "EGFLDTLVVLHRAGARLDVR", "down_seq": "AWGRLPVDLAEERGHRDVAG", "snv": [ { "evidence": [ { "id": "P42772", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772" } ], "glycoeffect": [], "subjects_tested": "4799", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "22006076", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D110", "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: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": "110", "end_pos": "110" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "86", "end_pos": "86" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "upstream", "id": "P42772-1.117.117", "categories": [ "snv_flag" ] } ], "glycosylation_flag": false, "snv_flag": true, "mutagenesis_flag": false, "phosphorylation_flag": false, "glycation_flag": false, "section_stats": [ { "table_id": "glycosylation", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_reported_with_glycan", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_predicted", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "glycosylation_automatic_literature_mining", "table_stats": [ { "field": "total", "count": 0 }, { "field": "total_sites", "count": 0 }, { "field": "n_linked_sites", "count": 0 }, { "field": "o_linked_sites", "count": 0 }, { "field": "n_linked_glycan_sites", "count": 0 }, { "field": "o_linked_glycan_sites", "count": 0 }, { "field": "n_linked_glycans", "count": 0 }, { "field": "o_linked_glycans", "count": 0 }, { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "phosphorylation", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "snv", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42772-1.117.117", "start_pos": 117, "end_pos": 117, "uniprot_canonical_ac": "P42772-1", "length": 138, "uniprot_id": "CDN2B_HUMAN", "protein_name": "Cyclin-dependent kinase 4 inhibitor B", "refseq_ac": "NP_004927", "refseq_name": "cyclin-dependent kinase 4 inhibitor B isoform 1", "gene_name": "CDKN2B", "gene_names_uniprotkb": "CDKN2B; MTS2", "gene_names_refseq": "CDK4I; CDKN2B; INK4B; MTS2; P15; TP15; p15INK4b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42772", "url": "https://www.uniprot.org/uniprotkb/P42772" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42772", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "V", "start_aa": "V", "up_seq": "VVLHRAGARLDVRDAWGRLP", "down_seq": "DLAEERGHRDVAGYLRTATG", "snv": [ { "evidence": [ { "id": "P42772", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772" } ], "glycoeffect": [], "subjects_tested": "1704", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "V", "sequence_mut": "M", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "22006055", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "V117", "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": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "86", "end_pos": "86" } ] } ], "categories": [ "snv_flag" ], "glycosylation": [], "mutagenesis": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 7, "direction": "downstream", "id": "P42772-1.110.110", "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": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_disease", "table_stats": [ { "field": "total", "count": 1 } ], "sort_fields": [ "subjects_tested", "subjects_positive", "frequency", "sequence_org", "sequence_mut", "comment", "chr_id", "chr_pos", "ref_nt", "alt_nt", "minor_allelic_frequency", "site_lbl" ] }, { "table_id": "snv_non_disease", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] }, { "table_id": "publication", "table_stats": [ { "field": "total", "count": 0 } ], "sort_fields": [] } ] }, { "id": "P42772-1.60.60", "start_pos": 60, "end_pos": 60, "uniprot_canonical_ac": "P42772-1", "length": 138, "uniprot_id": "CDN2B_HUMAN", "protein_name": "Cyclin-dependent kinase 4 inhibitor B", "refseq_ac": "NP_004927", "refseq_name": "cyclin-dependent kinase 4 inhibitor B isoform 1", "gene_name": "CDKN2B", "gene_names_uniprotkb": "CDKN2B; MTS2", "gene_names_refseq": "CDK4I; CDKN2B; INK4B; MTS2; P15; TP15; p15INK4b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42772", "url": "https://www.uniprot.org/uniprotkb/P42772" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42772", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "PNGVNRFGRRAIQVMMMGSA", "down_seq": "VAELLLLHGAEPNCADPATL", "snv": [ { "evidence": [ { "id": "P42772", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772" } ], "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 (4).", "chr_id": "9", "chr_pos": "22006226", "ref_nt": "G", "alt_nt": "A", "minor_allelic_frequency": "", "site_lbl": "R60", "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" } ] }, { "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": "P42772", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772" } ], "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": "9", "chr_pos": "22006225", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "R60", "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" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "snv", "site_list": [ { "start_pos": "110", "end_pos": "110" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "86", "end_pos": "86" } ] } ], "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": "P42772-1.86.86", "start_pos": 86, "end_pos": 86, "uniprot_canonical_ac": "P42772-1", "length": 138, "uniprot_id": "CDN2B_HUMAN", "protein_name": "Cyclin-dependent kinase 4 inhibitor B", "refseq_ac": "NP_004927", "refseq_name": "cyclin-dependent kinase 4 inhibitor B isoform 1", "gene_name": "CDKN2B", "gene_names_uniprotkb": "CDKN2B; MTS2", "gene_names_refseq": "CDK4I; CDKN2B; INK4B; MTS2; P15; TP15; p15INK4b", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "P42772", "url": "https://www.uniprot.org/uniprotkb/P42772" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [], "crossref": [ { "id": "P42772", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772", "database": "BioMuta", "categories": [ "Variation" ] } ], "site_seq": "D", "start_aa": "D", "up_seq": "LLHGAEPNCADPATLTRPVH", "down_seq": "AAREGFLDTLVVLHRAGARL", "snv": [ { "evidence": [ { "id": "P42772", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/P42772" } ], "glycoeffect": [], "subjects_tested": "9251", "subjects_positive": "1", "frequency": "0.0", "sequence_org": "D", "sequence_mut": "N", "comment": "Somatic mutation passed 1 filters: num. of cancers (3).", "chr_id": "9", "chr_pos": "22006148", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "D86", "disease": [ { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID: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": "110", "end_pos": "110" }, { "start_pos": "117", "end_pos": "117" }, { "start_pos": "60", "end_pos": "60" }, { "start_pos": "86", "end_pos": "86" } ] } ], "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": "O75398-1.432.432", "start_pos": 432, "end_pos": 432, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "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": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "iPTMnet", "id": "O75398", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75398" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] } ], "crossref": [ { "id": "GLY_001151", "url": "https://data.glygen.org/GLY_001151", "database": "GlyGen", "categories": [ "Other" ] }, { "id": "rs1352647775", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1352647775", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "rs1352647775", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1352647775#frequency_tab", "database": "TOPMed", "categories": [ "Other" ] }, { "id": "rs1352647775", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1352647775", "database": "gnomAD", "categories": [ "Other" ] }, { "id": "rs1859982135", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1859982135", "database": "dbSNP", "categories": [ "Other" ] }, { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75398", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75398", "database": "iPTMnet", "categories": [ "Other" ] } ], "site_seq": "T", "start_aa": "T", "up_seq": "PTSHPKIVLTSLPALAVPPP", "down_seq": "PTKAAPPALVNGLELSEPRS", "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": "Thr432", "evidence": [ { "id": "GLY_001151", "database": "GlyGen", "url": "https://data.glygen.org/GLY_001151" } ] } ], "snv": [ { "evidence": [ { "id": "rs1352647775", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1352647775" }, { "id": "rs1352647775", "database": "TOPMed", "url": "https://www.ncbi.nlm.nih.gov/snp/rs1352647775#frequency_tab" }, { "id": "rs1352647775", "database": "gnomAD", "url": "http://gnomad.broadinstitute.org/awesome?query=rs1352647775" } ], "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": "11", "chr_pos": "674745", "ref_nt": "G", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T432", "keywords": [ "ebi", "germline" ] }, { "evidence": [ { "id": "rs1859982135", "database": "dbSNP", "url": "https://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=rs1859982135" } ], "glycoeffect": [ "o-glyco-site-loss" ], "sequence_org": "T", "sequence_mut": "null", "comment": "Germline mutation passed 1 filters: o-glyco-site-loss (T->X).", "chr_id": "11", "chr_pos": "674751", "ref_nt": "p", "alt_nt": "null", "minor_allelic_frequency": "", "site_lbl": "T432", "keywords": [ "ebi", "germline" ] } ], "phosphorylation": [ { "kinase_uniprot_canonical_ac": "", "kinase_gene_name": "", "residue": "Thr", "comment": "Phosphothreonine", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" }, { "database": "iPTMnet", "id": "O75398", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/O75398" } ], "site_lbl": "Thr432" } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "glycosylation_flag", "snv_flag", "phosphorylation_flag" ], "mutagenesis": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 16, "direction": "upstream", "id": "O75398-1.448.448", "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": "O75398-1.0.0", "start_pos": 0, "end_pos": 0, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "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": "O75398", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75398" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "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": "O75398", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75398" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "crossref": [ { "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916", "database": "PubMed", "categories": [ "Other" ] }, { "id": "O75398", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75398", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948", "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": "38665916", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/38665916" }, { "id": "O75398", "database": "O-GlcNAc Database", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=O75398" }, { "id": "34019948", "database": "PubMed", "url": "https://glygen.org/publication/PubMed/34019948" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "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": "O75398-1.215.215", "start_pos": 215, "end_pos": 215, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.", "journal": "Nature structural biology", "date": "2001", "authors": "Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "crossref": [ { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "Y", "start_aa": "Y", "up_seq": "DPSVYDSELPVRCRNISGTL", "down_seq": "KNRLGSGGRGRCIKQGENWY", "mutagenesis": [ { "sequence_org": "Y", "sequence_mut": "Q", "comment": "Reduces transcription activation.", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "upstream", "id": "O75398-1.226.226", "categories": [ "mutagenesis_flag" ] }, { "distance": 15, "direction": "upstream", "id": "O75398-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75398-1.235.235", "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": "O75398-1.226.226", "start_pos": 226, "end_pos": 226, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.", "journal": "Nature structural biology", "date": "2001", "authors": "Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "crossref": [ { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RCRNISGTLYKNRLGSGGRG", "down_seq": "CIKQGENWYSPTEFEAMAGR", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Reduces transcription activation.", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 11, "direction": "downstream", "id": "O75398-1.215.215", "categories": [ "mutagenesis_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75398-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75398-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 20, "direction": "upstream", "id": "O75398-1.246.246", "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": "O75398-1.246.246", "start_pos": 246, "end_pos": 246, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.", "journal": "Nature structural biology", "date": "2001", "authors": "Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "crossref": [ { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "R", "start_aa": "R", "up_seq": "RCIKQGENWYSPTEFEAMAG", "down_seq": "ASSKDWKRSIRYAGRPLQCL", "mutagenesis": [ { "sequence_org": "R", "sequence_mut": "A", "comment": "Reduces transcription activation.", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75398-1.226.226", "categories": [ "mutagenesis_flag" ] }, { "distance": 16, "direction": "downstream", "id": "O75398-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 11, "direction": "downstream", "id": "O75398-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "upstream", "id": "O75398-1.250.250", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75398-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75398-1.253.253", "categories": [ "mutagenesis_flag" ] }, { "distance": 13, "direction": "upstream", "id": "O75398-1.259.259", "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": "O75398-1.250.250", "start_pos": 250, "end_pos": 250, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems.", "journal": "American journal of human genetics", "date": "2014", "authors": "Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, Vergult S, de Rocker N, Newhall KJ, Raghavan R, Reardon SN, Jarrett K, McIntyre T, Bulinski J, Ownby SL, Huggenvik JI, McKnight GS, Rose GM, Cai X, Willaert A, Zweier C, Endele S, de Ligt J, van Bon BW, Lugtenberg D, de Vries PF, Veltman JA, van Bokhoven H, Brunner HG, Rauch A, de Brouwer AP, Carvill GL, Hoischen A, Mefford HC, Eichler EE, Vissers LE, Menten B, Collard MW, de Vries BB", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "24726472", "url": "https://glygen.org/publication/PubMed/24726472" } ] }, { "title": "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.", "journal": "Nature structural biology", "date": "2001", "authors": "Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "crossref": [ { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24726472", "url": "https://glygen.org/publication/PubMed/24726472", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "QGENWYSPTEFEAMAGRASS", "down_seq": "DWKRSIRYAGRPLQCLIQDG", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Abolishes DNA-binding. Loss of DEAF1-promoter repression; when associated with A-253. Loss of transcriptional activation of EIF4G3; when associated with A-253. Loss of interaction with XRCC6; when associated with A-253. Loss of DNA binding; when associated with A-253.", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "24726472", "url": "https://glygen.org/publication/PubMed/24726472" }, { "database": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 20, "direction": "downstream", "id": "O75398-1.230.230", "categories": [ "snv_flag" ] }, { "distance": 15, "direction": "downstream", "id": "O75398-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 4, "direction": "downstream", "id": "O75398-1.246.246", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "upstream", "id": "O75398-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "upstream", "id": "O75398-1.253.253", "categories": [ "mutagenesis_flag" ] }, { "distance": 9, "direction": "upstream", "id": "O75398-1.259.259", "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": "O75398-1.252.252", "start_pos": 252, "end_pos": 252, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.", "journal": "Nature structural biology", "date": "2001", "authors": "Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "crossref": [ { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "W", "start_aa": "W", "up_seq": "ENWYSPTEFEAMAGRASSKD", "down_seq": "KRSIRYAGRPLQCLIQDGIL", "mutagenesis": [ { "sequence_org": "W", "sequence_mut": "Q", "comment": "Abolishes DNA-binding.", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 17, "direction": "downstream", "id": "O75398-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 6, "direction": "downstream", "id": "O75398-1.246.246", "categories": [ "mutagenesis_flag" ] }, { "distance": 2, "direction": "downstream", "id": "O75398-1.250.250", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "upstream", "id": "O75398-1.253.253", "categories": [ "mutagenesis_flag" ] }, { "distance": 7, "direction": "upstream", "id": "O75398-1.259.259", "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": "O75398-1.253.253", "start_pos": 253, "end_pos": 253, "uniprot_canonical_ac": "O75398-1", "length": 565, "uniprot_id": "DEAF1_HUMAN", "protein_name": "Deformed epidermal autoregulatory factor 1 homolog", "refseq_ac": "NP_001280563", "refseq_name": "deformed epidermal autoregulatory factor 1 homolog isoform b", "gene_name": "DEAF1", "gene_names_uniprotkb": "DEAF1; SPN; ZMYND5", "gene_names_refseq": "DEAF1; MRD24; NEDHELS; NUDR; SPN; VSVS; ZMYND5", "species": [ { "name": "Homo sapiens", "taxid": 9606, "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "common_name": "Human", "glygen_name": "Human", "reference_species": "Homo sapiens [9606]" } ], "publication": [ { "title": "Mutations affecting the SAND domain of DEAF1 cause intellectual disability with severe speech impairment and behavioral problems.", "journal": "American journal of human genetics", "date": "2014", "authors": "Vulto-van Silfhout AT, Rajamanickam S, Jensik PJ, Vergult S, de Rocker N, Newhall KJ, Raghavan R, Reardon SN, Jarrett K, McIntyre T, Bulinski J, Ownby SL, Huggenvik JI, McKnight GS, Rose GM, Cai X, Willaert A, Zweier C, Endele S, de Ligt J, van Bon BW, Lugtenberg D, de Vries PF, Veltman JA, van Bokhoven H, Brunner HG, Rauch A, de Brouwer AP, Carvill GL, Hoischen A, Mefford HC, Eichler EE, Vissers LE, Menten B, Collard MW, de Vries BB", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "24726472", "url": "https://glygen.org/publication/PubMed/24726472" } ] }, { "title": "The SAND domain structure defines a novel DNA-binding fold in transcriptional regulation.", "journal": "Nature structural biology", "date": "2001", "authors": "Bottomley MJ, Collard MW, Huggenvik JI, Liu Z, Gibson TJ, Sattler M", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" } ], "reference": [ { "type": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "crossref": [ { "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398", "database": "UniProtKB", "categories": [ "Protein" ] }, { "id": "24726472", "url": "https://glygen.org/publication/PubMed/24726472", "database": "PubMed", "categories": [ "Other" ] }, { "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895", "database": "PubMed", "categories": [ "Other" ] } ], "site_seq": "K", "start_aa": "K", "up_seq": "NWYSPTEFEAMAGRASSKDW", "down_seq": "RSIRYAGRPLQCLIQDGILN", "mutagenesis": [ { "sequence_org": "K", "sequence_mut": "A", "comment": "Abolishes DNA-binding. oss of DEAF1-promoter repression; when associated with A-250. Loss of transcriptional activation of EIF4G3; when associated with A-250. Loss of interaction with XRCC6; when associated with A-250. Loss of DNA binding; when associated with A-250.", "evidence": [ { "database": "UniProtKB", "id": "O75398", "url": "https://www.uniprot.org/uniprotkb/O75398" }, { "database": "PubMed", "id": "24726472", "url": "https://glygen.org/publication/PubMed/24726472" }, { "database": "PubMed", "id": "11427895", "url": "https://glygen.org/publication/PubMed/11427895" } ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "432", "end_pos": "432" } ] }, { "type": "mutagenesis", "site_list": [ { "start_pos": "215", "end_pos": "215" }, { "start_pos": "226", "end_pos": "226" }, { "start_pos": "246", "end_pos": "246" }, { "start_pos": "250", "end_pos": "250" }, { "start_pos": "252", "end_pos": "252" }, { "start_pos": "253", "end_pos": "253" }, { "start_pos": "302", "end_pos": "302" }, { "start_pos": "304", "end_pos": "304" }, { "start_pos": "538", "end_pos": "538" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "115", "end_pos": "115" }, { "start_pos": "184", "end_pos": "184" }, { "start_pos": "230", "end_pos": "230" }, { "start_pos": "235", "end_pos": "235" }, { "start_pos": "259", "end_pos": "259" }, { "start_pos": "25", "end_pos": "25" }, { "start_pos": "274", "end_pos": "274" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": "29", "end_pos": "29" }, { "start_pos": "338", "end_pos": "338" }, { "start_pos": "354", "end_pos": "354" }, { "start_pos": "365", "end_pos": "365" }, { "start_pos": "399", "end_pos": "399" }, { "start_pos": "410", "end_pos": "410" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "463", "end_pos": "463" }, { "start_pos": "479", "end_pos": "479" }, { "start_pos": "508", "end_pos": "508" } ] }, { "type": "phosphorylation", "site_list": [ { "start_pos": "171", "end_pos": "171" }, { "start_pos": "176", "end_pos": "176" }, { "start_pos": "179", "end_pos": "179" }, { "start_pos": "432", "end_pos": "432" }, { "start_pos": "448", "end_pos": "448" } ] } ], "categories": [ "mutagenesis_flag" ], "glycosylation": [], "snv": [], "phosphorylation": [], "glycation": [], "biomarkers": [], "neighbors": [ { "distance": 18, "direction": "downstream", "id": "O75398-1.235.235", "categories": [ "snv_flag" ] }, { "distance": 7, "direction": "downstream", "id": "O75398-1.246.246", "categories": [ "mutagenesis_flag" ] }, { "distance": 3, "direction": "downstream", "id": "O75398-1.250.250", "categories": [ "mutagenesis_flag" ] }, { "distance": 1, "direction": "downstream", "id": "O75398-1.252.252", "categories": [ "mutagenesis_flag" ] }, { "distance": 6, "direction": "upstream", "id": "O75398-1.259.259", "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" ] } ] } ]